Transmembrane protein amigo and uses thereof

ABSTRACT

The present invention provides methods and compositions relating to vertebrate AMIGO, AMIGO2, AMIGO3, collectively vertebrate AMIGO polypeptides, related nucleic acids, and polypeptide domains thereof having vertebrate AMIGO-specific structure and activity, and modulators of vertebrate AMIGO function.

FIELD OF THE INVENTION

The present invention generally relates to the field of geneticengineering and more particularly to transmembrane proteins implicatedin axon tract development.

BACKGROUND OF THE INVENTION

Development of the nervous system with billions of connections is one ofthe most complex and fascinating phenomena in nature. One key feature inthis event is the guidance of the neuronal growth cones to theirappropriate targets. A wide variety of soluble matrix and cell surfacemolecules have been found to be involved in axonal growth and inassociation of axons to form mature fiber tracts (for reviews, seeTessier-Lavigne and Goodman, 1996; Drescher et al., 1997).

Within the peripheral nervous system (PNS), injured nerve fibers canregrow over long distances, with eventual excellent recovery offunction. Within the past 15 years, neuroscientists have come to realizethat this is not a consequence of intrinsic differences between thenerve cells of the peripheral and central nervous system; remarkably,neurons of the CNS will extend their axons over great distances if giventhe opportunity to grow through a grafted segment of PNS (e.g., sciaticnerve). Therefore, neurons of the CNS retain a capacity to grow if giventhe right signals from the extracellular environment. Factors whichcontribute to the differing growth potentials of the CNS and PNS includepartially characterized, growth-inhibiting molecules on the surface ofthe oligodendrocytes that surround nerve fibers in the CNS, but whichare less abundant in the comparable cell population of the PNS (Schwanncells); molecules of the basal lamina and other surfaces that fostergrowth in the PNS but which are absent in the CNS (e.g., laminin); andtrophic factors, soluble polypeptides which activate programs of geneexpression that underlie cell survival and differentiation. Althoughsuch trophic factors are regarded as essential for maintaining theviability and differentiation of nerve cells, the particular ones thatare responsible for inducing axonal regeneration in the CNS remainuncertain. As a result, to date, effective treatments for CNS injurieshave not been developed.

Immunoglobulin superfamily proteins form the most diverse and studiedclass of molecules, which have been shown to participate incontact-dependent regulation of neurite outgrowth, axon guidance andsynaptic plasticity (for reviews see, Schachner; 1997; Walsh andDoherty, 1997; Stoeckli and Landmesser, 1998; Van Vactor, 1998).Extracellular proteins containing leucine-rich repeats (LRRs) have alsobeen shown to participate in axon guidance. For instance, Slit proteinscontaining LRR domains act as midline repellents for commissural axonsthrough the Robo (Roundabout) receptor (Battye et al., 1999; Brose etal., 1999) and recently Battye et al. (2001) showed that the interactionof Slits with their Robo receptors was due to LRRs found in Slits.Furthermore, Pusch et al. (2000) showed that the disease called X-linkedcongenital stationary night blindness (XLCSNB) maps to a gene, whichcodes only the LRR containing protein Nyctalopin in retina. Recently thereceptor for axonal regeneration inhibitor Nogo (Chen et al., 2000) wasfound to be a GPI-linked cell surface protein where the onlyrecognizable motifs are LRR domains (Fournier et al., 2001).

Amphoterin (also known as HMGB1) is a heparin-binding protein that wasisolated from perinatal rat brain as a neurite outgrowth-promotingfactor (Rauvala and Pihlaskari, 1987) enriched in the growth cones ofneuronal cells. Amphoterin has been proposed to be an autocrine factorin invasive cell or growth cone migration due to binding to the cellsurface receptors (RAGE and sulphated glycan epitopes) and to activationof proteolysis of ECM through binding of plasminogen and it's activatorsto amphoterin (for reviews see Rauvala et al., 2000; Muller et al.,2001).

To examine the role of amphoterin in cell motility, especially inneurite outgrowth, we searched for genes that are induced on amphoterinmatrix by using mRNA differential display. In this invention, wedescribe the cloning and functional characterization of a novel proteinnamed as AMIGO (AMphoterin Induced Gene and Orphan receptor). Cloning ofAMIGO gave us sequence data to clone two other related proteins (AMIGO2and AMIGO3); together these three proteins form a novel family oftransmembrane proteins. The predicted amino acid sequences of the AMIGOssuggest that they are type I transmembrane proteins containing a signalsequence for secretion and a transmembrane domain. Interestingly, theextracellular part of the AMIGOs contains six leucine-rich repeats(LRRs) flanked by cysteine-rich LRR N- and C-terminal domains and oneimmunoglobulin domain close to the transmembrane region. This twin motifstructure defines the AMIGOs as members of both the immunoglobulin andthe leucine-rich repeat superfamilies.

Amphoterin

Amphoterin is a protein, which was isolated from perinatal rat brainaccording to its ability to promote neurite outgrowth (Rauvala andPihlaskari, 1997). Amphoterin is a dipolarised molecule, which containsboth positively and negatively charged regions. This dipolar nature ofamphoterin renders it very adhesive molecule, which binds for example toheparin and other sulphated glycans.

Amphoterin is also found to localize in nucleus and to bind DNA and inthis role it is called as HMG1 (Bianchi et al., 1989). In subsequentstudies amphoterin has been shown to localize diffusibly inside the cellbut when the cell starts to grow projections amphoterin is localizedinto the tips of the projections (Merenmies et al., 1991; Parkkinen etal., 1993). Although amphoterin lacks the signal sequence for secretion,it has been shown to be present also in the extracellular matrix (ECM).In vitro amphoterin has been shown to localize to the surface of theneurons (Rauvala and Pihlaskari, 1997; Rauvala et al., 1988) andamphoterin has been shown to be a ligand for the cell surface receptorRAGE (Hori et al., 1995). During the endotoxin shock large quantities ofamphoterin has been shown to accumulate into the human plasma (Wang etal., 1999). During the period when the red blood cells are maturingamphoterin is secreted into the ECM, where it is believed to work as adifferentiation factor (Passalacqua et al., 1997). It is also suggestedthat the amphoterin secreted from glial cells works as a factor betweenthe interaction of glia and neurons (Passalacqua et al., 1998; Dastonand Ratner, 1994).

Amphoterin is highly expressed in neurons and glial cells in developingnervous system and generally in non-mature cells. Amphoterin is alsohighly expressed in monocytes and macrophages and often in transformedcells. Amphoterin is thought to be involved in invasive migration ofcells. Amphoterin binds plasminogen and plasminogen activators and thisbinding has been shown to activate the formation of the plasmin and alsodegradation of amphoterin (Parkkinen and Rauvala, 1991; Parkkinen etal., 1993). At the cell surface level amphoterin binds to thetransmembrane protein RAGE and some proteoglycans (like Syndecan-1) andsulphoglycolipids. The multiligand protein RAGE (Receptor of advancedglycation end products) is a member of immunoglobulin superfamily.Amphoterin stimulates the neurite outgrowth via RAGE dependentsignalling and the both proteins also localize in same areas of thedeveloping nervous system (Hori et al., 1995). It has been suggestedthat amphoterin works as an autocrine and/or paracrine factor ininvasive migration; amphoterin binds to its receptors and activates boththe proteolysis of the ECM and the reorganization of the cytoskeleton(Rauvala et al., 2000; Rauvala et al., 1988). It has been shown that byinhibiting the interaction between amphoterin and RAGE the growth andthe invasiveness of the tumour could be reduced.

Immunoglobulin Domains

IgG domain is one of the most common extracellular protein motifs. Itwas first discovered from antibody molecules. In addition of antibodymolecules, many cell adhesion molecules, cell surface receptors and someintracellular muscular proteins contain IgG domains. IgG domain is about70-110 amino acids long usually containing two cysteines separated by55-77 amino acids, it forms 7-10 beta sheets, and is a tightly packedglobular structure with hydrophobic residues inside and hydrophilicoutside. The structure is often stabilized by disulfide bridge betweenconserved cysteines (Walsh and Doherty 1997; Williams and Barclay 1988).

In sequence level IgG domains differ greatly. The homology betweendifferent IgG domains within the same protein may share only 10-30%amino acid similarity. Although all IgG domains share the same corestructure, two beta sheets stacked together, the other features can varyconsiderably. In spite of variability within IgG domains they can beclassified in categories. Originally they were classified as C1, C2 andV, and later Group I was added (Williams and Barclay 1988). Thestability of IgG domain may explain why it commonly resides inextracellular space, it is resistant to proteolytic and oxidativeenvironment. Extracellular IgG domain containing molecules may functionin cell adhesion and in recognition and binding of molecules. IgG domainseems to interact with any parts of its domain surface. (Williams andBarclay 1988)

IgG domain containing proteins form so called immunoglobulingsuperfamily of proteins, which is the most common family of cell surfaceproteins. Sequence analysis has shown that 765 human proteins belong tothis family, in flyes there are 140 and in worms 64 proteins (Venter etal 2001). The members of IgG family encode proteins that are involved incell recognition and adhesion such as antibody molecules, T-cellreceptors, growth factor receptors, many adhesion molecules and neuriteoutgrowth promoting receptors. IgG domain adhesion molecules oftenconsist of several consequent IgG domains and type III fibronectin likedomains (Crossin and Krushel 2000).

Neuronal members of immunoglobuling superfamily act as receptor andadhesion molecules and their role have been especially indicated in manyimportant functions related to axonal growth and guidance. Adhesionmolecules have important roles during the neuronal development wheremany interactions need to be coordinated in precise manner, for exampleNCAM and L1 which function during axonal growth and guidance (Walsh andDoherty 1997). Other members include receptor for FGF (FGFR, Trk familyof neurotrophic factor receptors, Eph receptors, Robo (Roundabout) thatmediates the functions of Slit and DCC (Deleted in colorectal carcinoma)that interacts with netrins (Tessier-Lavigne and Goodman 1996; Brose andTessier-Lavigne 2000).

Axonal IgG cell adhesion molecules may interact in homophilic orheterophilic way with other IgG family members. The binding partner maylocalize at the same cell membrane, in adjacent cell membrane or inextracellular space. Many IgG proteins form a very complex network ofcellular interactions where they can even have partially overlappingfunctions. They may also compete for the same ligands by modulatingtheir binding affinity to other ligands (Brummendorf and Lemmon 2001).

Immunoglobulin superfamily members involved in myelinization are MAG(myelin-associated glycoprotein) and P0 although their precise actionsare not known. MAG's functions have been shown to be associated withinhibition of regeneration of CNS neurons or it can either activate orinhibit the neurite growth of certain neurons. Approximately half of theall protein in myelin consists of P0 protein which is a homophilic celladhesion molecule thought to be involved in interconnection of cellmembranes of myelin sheath (Brummendorf and Rathjen 1994).

LRR Domains

Leucine rich repeats (LRR) are 20-29 amino acid long sequence motifscharacterized by repetition of hydrophobic residues, especially leucineand that are separated by conserved distance. The sequence repeat isfound in several times in protein and this region of repeats is calledLRR domain. LRR contains conserved 11 amino acid long consensussequence, LxxLxLxxzxL where x stands for any amino acid, z for N orcysteine and L for leucine, valine, isoleucine or phenylalanine. LRRproteins contain usually many LRR domains and can contain up to 30repeats (chaoptin). LRR domains are not always identical to consensussequence and may therefore contain gaps, have different lengths or aminoacid compositions (Kobe and Deisenhofer 1994).

To prevent the sole hydrophobic core of LRR domain from interactingdirectly with solvents it is flanked by several cysteine residues at itsN and/or C terminal sides (LRRNT, LRRCT domains). Sequence analysis hasrevealed that there are four different C terminal cysteine rich domainsand one N terminal one (Kobe and Kajava 2001; Kajava 1998). Thesecysteine domains are only found from extracellular proteins andcysteines form intermolecular disulfide bridges (Kresse et al 1993;Hashimoto et al 1991).

LRR domain proteins are located in various places in cells and they havedifferent functions. Eukaryotic LRR proteins can be found in nucleus,cytoplasm, cell membrane as well as in extracellular space and they canact as hormone receptors, subunits of enzymes, cell adhesion moleculesand in cell recognition (Kobe and Kajava 2001). Moreover, they mediatevarious cellular functions such as signal transduction, intracellulartransport, and DNA repair, recombination and transcription (Buchanan andGay 1996).

LRR proteins can be divided into at least 7 different subclassesaccording to the length of LRR and the composition of consensussequence. Subclasses are RI-like, SDS22-like, cysteine containing,bacterial, typical, plant specific and TpLRR (Kobe and Kajava 2001).Former three are intracellular whereas latter four are found in cellularmembranes or in the extracellular space.

LRR domains are thought to have a role in protein-protein interactions.For example, chaoptin is a cell surface protein which consists of LRRdomains, is attached to cell membrane via lipid anchor, and has beenshown to mediate homophilic cell adhesion (Reinke et al 1988; Krantz andZipursky 1990).

Extracellular matrix contains several homologous small proteglycanswhose sequences are composed 70-80% of LRR domains. These smallproteoglycans are composed of N-terminal glycosaminoglycans and variableamounts of LRRs that are flanked by LRRNT and LRRCT domains.Proteoglycans such as biglycan binds to laminin and fibronectin whereasdecorin and fibromodulin bind to type I and II collagens (Svensson et al1995). Axonal growth modulating molecule Slit contains LRR domain, EGFrepeats, laminin like G domain and LRRNT and LRRCT domains. Only LRRdomain of Slit is needed for its binding to Robo in vitro as well asmediating repulsive signalling in vivo (Battye et al 2001).

Although several LRR proteins are expressed in the nervous system onlyfew of those functions or binding partners are known. The bestcharacterized neuronal LRR proteins are Drosophila's connectin,capricious and chaoptin. Connectin is a GPI (glycosyl phosphatidylinositol) linked cell adhesion protein that has a role during thedevelopment of neuromuscular junction. It contains 10 LRR domainsflanked by LRRCT domain. During the formation of neuromuscular junctionconnectin is expressed in surfaces of certain muscle cells andconcomitantly in their innervating motor neurons where the expression isespecially seen in growth cones. During synapse formation connectinlocalizes in junctional areas but during synapse maturation connectinexpression is downregulated. In vitro experiments have indicatedincreased homophilic cell adhesion between connectin transfected S2cells (Nose et al 1992; Meadows et al 1994). Moreover, in vivo studieshave supported its role as attractive neuronal growth modulatingprotein. When connectin is misexpressed in all muscular cells aberrantneuromuscular junction formation occurs (Yu et al 2000).

Capricious is a cell membrane protein sharing similarities with thefunctions of connectin in neuromuscular junction formation. It contains12 LRR domains flanked by LRRCT and LRRNT domains. It probably mediatescell-to-cell signalling processes during the formation of theneuromuscular junction since in vitro studies have not supported itshomophilic adhesion (Shishido et al 1998).

Chaoptin is a photoreceptor cell specific adhesion molecule whichcontains 30-40 LRR domains and is linked to cell membrane via GPIanchor. It mediates homophilic cell adhesion and is needed for theproper formation of a photoreceptor cell (Krantz and Zipursky 1990).

Slit proteins are conserved, secreted into extracellular space andprovide guidance during axonal growth and branching. Slit proteinsconsist of several LRR domains, EGF like repeats, laminin like G-domainand LRRNT domain (Brose and Tessier-Lavigne 2000). Slit was discoveredfrom fruit fly where it repels axonal growth (Rothberg et al 1990; Kiddet al 1999). Slit is produced by glial cells of midline and it is neededfor the formation of axonal tracts crossing the midline as well aspositioning of horizontal lateral tracts. Biological functions of Slitare mediated by Robo which is a cell membrane receptor. LRR domains ofSlit bind to Robo in vitro and LRR domains are needed for Slit'srepulsive signalling (Battye et al 2001). Three mammalian Slits andRobos have been cloned. In addition, Slit binds to laminin-1, netrin-1,and glypican-1 (Brose et al 1999; Liang et al 1999).

Nogo receptor (NogoR) is CNS receptor protein found in myelin andresponsible for the inhibition of axonal regeneration. NogoR consists of8 LRR domains flanked by LRRCT domain and it is attached to cellmembrane via GPI anchor. It binds to Nogo-66 while inhibiting axonalgrowth (Grandpre and Strittmatter 2001; Fournier et al 2001).

OMgp is oligodendrocyte-myelin glycoprotein found in CNS myelin and cellmembranes of oligodendrocytes. It is 110 kDa GPI-anchored cell membraneprotein containing at least 6 LRR domains and LRRNT domain (Mikol et al1988 and 1990). Like Nogo, OMgp inhibits axonal regeneration in themammalian CNS. Until recently OMgp has been shown to bind NogoR whileinhibiting axonal regeneration (Wang et al 2002).

LRR- and Ig-Domains Containing Proteins

Some transmembrane proteins of nervous system contain both LRR- andIg-domains, which are discussed below.

Kekkon and ISLR

Drosophilae (fruit fly) has gene family called kekkon, which codestransmembrane proteins with both LRR- and Ig-domains. The extracellularpart of the kekkon1 (kek1) and kekkon2 (kek2) contains six LRRs flankedwith LRRNT and LRRCT domains. They also contain one type C2 Ig-domainclose to transmembrane region and large intracellular tail. Both genesare expressed in developing central nervous system (CNS) and the kekkon1is also present in developing ovary (Musacchio and Perrimon, 1996). Thekek1 has been shown to inhibit the function of the epidermal growthfactor receptor (EGFR) in oogenesis (Ghiglione, 1999). Interestingly,only the extracellular part and transmembrane domains of the kek1protein are needed for EGFR inhibition.

The transmembrane protein ISLR has same kind of domain structure as thekekkon proteins. The extracellular part of the ISLR contains six LRRslined with LRRNT and LRRCT domains. It also contains one type C2Ig-domain close to transmembrane region but it does not containintracellular part. The ISLR has been cloned from humans and mice. TheISLR is expressed in various tissues like retina, heart, thymus andspinal cord (Nagasawa et al., 1999; Nagasawa et al., 1997).

Trk-Receptors

Neurotrophin receptors TrkA, TrkB and TrkC are receptor tyrosinekinases, in which the extracellular part contains three LRR-areas andeach area is flanked with LRRNT and LRRCT domains. The extracellularpart contains also two Ig-domains. The intracellular parts ofTrk-receptors contain tyrosine kinase domain. The ligands ofTrk-receptors are neurotrophins, which are important factors indevelopment and in maintenance of central and peripheral nervous system.The binding of the neurotrophins into the Trk-receptor dimerazes thereceptor and the tyrosine kinase domain is autophosphorylated and thisphosphorylation activates several signalling cascades (Kaplan andMiller, 1997). Originally, some studies indicated that the LRR-areas ofthe Trk-receptors are the ligand binding domains (Windisch et al., 1995;Windish et al., 1995). Recently it has been shown that the Ig-domain ofthe TrkA receptor closest to the cell surface is the one, which bindsthe Nerve growth factor (NGF)(Holden et al., 1997; Perez et al., 1995;Robertson et al., 2001; Urfer et al., 1995; Wiesmann et al., 1999).

NLRRs, Pal and LIG-1

Neuronal Leucine-rich repeat proteins (NLRRs) are transmembrane proteinsexpressed in nervous tissues. The extracellular part of the NLRRscontains 12 LRRs flanked with LRRNT and LRRCT domains, one Ig-domain andtype III fibronectin like domain. Similar NLRR proteins have been foundfrom mouse, rat, zebra fish, frog and human (Hayata et al., 1998;Taniguchi et al., 1996: Taguchi et al., 1996; Bormann et al., 1999;Fukamachi et al., 1998). In zebra fish one member of NLRR family isexpressed specifically during the axonal regeneration after injury(Hayata et al., 1998). Unlike in adult mammalian CNS the neurons of thefish could raise new neurons into the injured area. In mouse NLRR-3 genehas been shown to be induced after cortical injury (Ishii et al., 1996).

Pal is a transmembrane protein, which is expressed specifically inretina. The extracellular part of the pal contains five LRRs flankedwith LRRNT and LRRCT domains, one type C2 Ig-domain and type IIIfibronectin like domain. In adult retina pal is expressed byphotoreceptor cells, where protein is believed to localize in disks. Thefunction of the pal is not yet known, but it has been shown to formhomodimers (Gomi et al., 2000).

LIG-1 is also a transmembrane protein, which contains both LRRs andimmuoglobulin domains. The extracellular part of the LIG-1 contains 15LRRs and three type C2 Ig-domains. The intracellular part of the LIG-1is 270 amino acids long and it does not contain any known domains. LIG-1is expressed highly in brain both in mice and humans. In mouse the LIG-1expression is localized in particular subpopulations of neuronal supportcells; in cerebellum LIG-1 is localized in Bergman glia cells (Nilssonet al., 2001; Suzuki et al., 1996).

In this invention we have characterized AMIGO, AMIGO2 and AMIGO3, themembers of the protein family that is highly expressed in the nervoussystem. We disclose that AMIGOs mediate cell-to-cell interactions via ahomophilic and heterophilic mechanism during the development of thefiber tracts of the nervous system.

Epidermal Growth Factor Receptor

Epidermal growth factor receptor (EGFR) is a 170 kDa transmembraneglycoprotein which possesses the intrinsic tyrosine kinase activity(Cohen et al., 1982). EGFR exerts a great variety of biologicalfunctions including cell survival, mitogenic response, differentiationand cell motility (Khazaie et al., 1993). Many ligands for EGFR havebeen identified including epidermal growth factor (EGF), transforminggrowth factor alpha (TGF-α), amphiregulin (AR), epiregulin (EP),Batacellulin (BTC), Heparin-binding EGF-like growth factor (HB-EGF) andSchwannoma-derived growth factor (SDGF). The EGF-family of peptides issignificantly involved in the regulation of mammary-gland development,morphogenesis and lactation, and also implicated in the pathogenesis ofhuman breast cancer (Normanno and Ciardiello, 1997).

Epidermal Growth Factor Receptor (EGFR) (SEQ ID NOS:21-24) is a specificreceptor for epidermal growth factor (EGF) (SEQ ID NOS:25-28) andtransforming growth factor-α (TGF-α) (SEQ ID NOS:29-32). When thesemitogenic polypeptides bind to EGFR, tyrosine kinase activity of thereceptor is induced, and this in turn triggers a series of events whichregulate cell growth. A number of malignant and non-malignant diseaseconditions are now believed to be associated with EGFR, particularlyaberrant expression of EGFR. Aberrant expression includes both increasedexpression of normal EGFR and expression of mutant EGFR. Overexpressionof EGFR is found in many human tumors including most glioblastomas andbreast, lung, ovarian, colorectal, bladder, pancreatic, squamous celland renal carcinomas. Elevated EGFR levels correlate with poor prognosisin human tumors. The sequence of the mRNA encoding human EGFR is known(Ullrich et al., Nature, 1984, 309, 418; GenBank Accession NumberNM_(—)005228). The gene encoding EGFR is also known as c-erb-B1. TwoEGFR transcripts typically appear on Northern blots, one measuring 10 kband one measuring 5.6 kb.

One role the EGF receptor system may play in the oncogenic growth ofcells is through autocrine-stimulated growth. If cells express the EGFRand secrete EGF and/or TGF-α then such cells could stimulate their owngrowth. Since some human breast cancer cell lines and tumors expressEGFR (Osborne, et al., J. Clin. Endo. Metab., 55:86-93 (1982);Fitzpatrick, et al., Cancer Res., 44:3442-3447 (1984); Filmus, et al.,Biochem. Biophys. Res. Commun., 128:898-905 (1985); Davidson, et al.,Mol. Endocrinol., 1:216-223 (1987); Sainsbury, et al., Lancet, i:1398-1402 (1987); Perez, et al., Cancer Res. Treat., 4:189-193 (1984))and secrete TGF.alpha. A (Bates, et al., Cancer Res., 46:1707-1713(1986); Bates, et al., Mol. Endocrinol., 2:543-555 (1988)), an autocrinegrowth stimulatory pathway has been proposed in breast cancer (Lippman,et al., Breast Cancer Res. Treat., 7:59-70 (1986)).

A number of inhibitors of EGFR have been shown to be effective ininhibiting the growth of human tumor cells. Monoclonal antibodies toEGFR and drugs which inhibit EGFR tyrosine kinase activity can inhibitthe growth of human cancer cell xenografts in nude mice. Normanno etal., Clin. Cancer Res., 1996, 2, 601 and Grünwald et al, J Nat CancerInst, 2003, 95:851. The drug PD153035, which inhibits EGFR tyrosinekinase activity, can inhibit the growth of A431 cells in nude mice, andtyrphostins, which inhibit the activity of EGFR as well as othertyrosine kinases, have been shown to inhibit the growth of squamouscarcinoma in nude mice. Kunkel et al., Invest. New Drugs, 1996, 13, 295and Yoneda et al., Cancer Res., 1991, 51, 4430. Additonal small moleculetyrosine kinase inhibitors include ZD1839, OSI-774, CI-1033, PKI-166,GW2016, EKB-569, PD168393, AG-1478, and CGP-59326A (Grünwald et al, JNat Cancer Inst, 2003, 95:851 incorporated herein by reference in theentirety.

Furthermore, EGFR expression is frequently accompanied by the productionof EGFR-ligands, TGF-α and EGF among others, by EGFR-expressing tumorcells which suggests that an autocrine loop participates in theprogression of these cells (Baselga, et al. (1994) Pharmac. Therapeut.64:127-154; Modjtahedi, et al. (1994) Int. J. Oncology. 4:277-296).Blocking the interaction between such EGFR ligands and EGFR thereforecan inhibit tumor growth and survival (Baselga, et al. (1994) Pharmac.Therapeut. 64:127-154).

A variety of approaches can be used to target EGFR such as usingmonoclonal antibodies to compete with the binding of activating ligandsto the extracellular domain of the receptor, using small moleculeinhibitors ot the intracellular tyrosine kinase domain of the receptor,using immunotoxin conjugates to deliver toxins that target EGFR totumour cells, reducing the level of EGFR through the use of antisenseoligonucleotides, and inhibiting downstream effectors of the EGFRsignalling network. Despite the foregoing approaches, the need existsfor new compounds against EGFR which are effective at treating and/orpreventing diseases related to expression of EGFR.

SUMMARY OF THE INVENTION

The present invention provides methods and compositions relating tovertebrate AMIGO, AMIGO2, AMIGO3, collectively vertebrate AMIGOpolypeptides, related nucleic acids, and polypeptide domains thereofhaving vertebrate AMIGO-specific structure and activity, and modulatorsof vertebrate AMIGO function. Vertebrate AMIGO polypeptides can regulatecell, especially nerve cell, function and morphology. The polypeptidesmay be produced recombinantly from transformed host cells from thesubject vertebrate AMIGO polypeptide encoding nucleic acids or purifiedfrom mammalian cells. The invention provides isolated vertebrate AMIGOhybridization probes and primers capable of specifically hybridizingwith natural vertebrate AMIGO genes, vertebrate AMIGO-specific bindingagents such as specific antibodies, and methods of making and using thesubject compositions in diagnosis (e.g. genetic hybridization screensfor vertebrate AMIGO transcripts), therapy (e.g. to modulate nerve cellgrowth) and in the biopharmaceutical industry (e.g. as immunogens,reagents for isolating vertebrate AMIGO genes and polypeptides andreagents for screening chemical libraries for lead pharmacologicalagents.

In one embodiment, the invention contemplates in vitro methods and kitsfor culturing neuronal cells under conditions where the subjectpolypeptides are used to promote neurite outgrowth, and can includemethods for detecting the presence and amount of stimulation of neuriteoutgrowth in the cultured neuronal cells. AMIGO proteins andpolypeptides disclosed herein are useful according to thewithin-disclosed methods and may be included in the kits that are alsodescribed herein.

Appropriate cells are prepared for use in a neurite outgrowth assay. Forexample, a preparation of hippocampal neurons is disclosed in theExamples. Before beginning the assay, the cells may be resuspended,added to substrate-coated dishes, and placed under predetermined assayconditions for a preselected period of time. After the attachment andgrowth period, the dishes may be rinsed to remove unbound cells, fixed,and viewed—e.g., by phase contrast microscopy.

Preferably, a plurality of cells are analyzed for each substrate. Cellsare then “judged” based on predetermined criteria. For example, cellsmay be considered neurite-bearing if the length of the processes aregreater than one cell diameter. The percent of cells that are sproutingneurites is preferably determined, as is the average neurite length. Aparticularly preferred neurite outgrowth assay method is disclosed inthe Examples.

The proteins and polypeptides of the present invention are thereforeuseful in a variety of applications relating to cell and tissuecultures.

For example, in one embodiment, a method of inhibiting neurite outgrowthof neuronal cells in a cell culture system comprises the steps of (1)introducing neuronal cells into tissue culturing conditions comprising aculture medium; and (2) introducing an AMIGO polypeptide of the presentinvention into the culture medium in an amount effective to inhibitneurite outgrowth in the culture.

In another embodiment, a method of promoting neurite outgrowth ofneuronal cells in a cell culture system comprises the steps of (1)immobilizing on the substrate a polypeptide of the present inventionhaving neurite outgrowth-promoting activity; and (2) contacting neuronalcells with the substrate under tissue culturing conditions.

In another embodiment, a method of promoting neurite outgrowth ofneuronal cells in a cell culture system comprises the steps of (1)introducing an AMIGO nucleic acid encoding peptide having neuriteoutgrowth-promoting activity of the present invention; (2) immobilizingon the substrate a polypeptide of the present invention having neuriteoutgrowth-promoting activity; and (3) culturing said neuronal cellsunder tissue culturing conditions.

The invention also discloses compositions comprising polypeptidesexhibiting a neurite outgrowth-promoting in substantially pure form. Invarious embodiments, the polypeptides are derived from segments of anAMIGO protein.

In another embodiment, a composition according to the present inventioncomprises a subject polypeptide in substantially pure form and attachedto a solid support or substrate.

The solid support may be a prosthetic device, implant, or suturingdevice designed to have a surface in contact with neuronal cells or thelike; further, it may be designed to lessen the likelihood of immunesystem rejection, wherein said surface of said device is coated with asubject polypeptide or other material designed to ameliorate rejection.

The AMIGO proteins, polypeptides, and nucleid acids disclosed herein arealso useful in a variety of therapeutic applications as describedherein.

The present therapeutic methods are useful in treating peripheral nervedamage associated with physical or surgical trauma, infarction, toxinexposure, degenerative disease, malignant disease that affectsperipheral or central neurons, or in surgical or transplantation methodsin which new neuronal cells from brain, spinal cord or dorsal rootganglia are introduced and require stimulation of neurite outgrowth fromthe implant and innervation into the recipient tissue. Such diseasesfurther include but are not limited to CNS lesions, gliosis, Parkinson'sdisease, Alzheimer's disease, neuronal degeneration, and the like. Thepresent methods are also useful for treating any disorder which inducesa gliotic response or inflammation.

In treating nerve injury, contacting a therapeutic composition of thisinvention with the injured nerve soon after injury is particularlyimportant for accelerating the rate and extent of recovery.

Thus the invention contemplates a method of promoting neurite outgrowthin a subject, or in selected tissues thereof, comprising administeringto the subject or the tissue a physiologically tolerable compositioncontaining a therapeutically effective amount of a neuriteoutgrowth-promoting AMIGO compound of the present invention.

In preferred methods, a human patient is the subject, and theadministered polypeptide comprises extracellular domain of human AMIGO.In anothere preferred method, a human patient is the subject, and theadministered nucleic acid encodes AMIGO extracellular domain of humanAMIGO.

In one embodiment, a severed or damaged nerve may be repaired orregenerated by surgically entubating the nerve in an entubalation devicein which an effective amount of a neurite outgrowth-promotingpolypeptide of this invention can be applied to the nerve.

In a related embodiment, a polypeptide of the invention can beimpregnated into an implantable delivery device such as a cellulosebridge, suture, sling prosthesis or related delivery apparatus. Such adevice can optionally be covered with glia, as described by Silver, etal, Science 220:1067-1069, (1983), which reference is herebyincorporated by reference.

Therapeutic compositions of the present invention may include aphysiologically tolerable carrier together with at least one species ofneurite outgrowth-promoting polypeptide of this invention as describedherein, dispersed therein as an active ingredient. In a preferredembodiment, the therapeutic composition is not immunogenic whenadministered to a human patient for therapeutic purposes.

For the sake of simplicity, the active agent of the therapeuticcompositions described herein shall be referred to as a “neuriteoutgrowth-promoting polypeptide”. It should be appreciated that thisterm is intended to encompass a variety of AMIGO polypeptides includingfusion proteins, synthetic polypeptides, and fragments of naturallyocurring proteins, as well as derivatives thereof, as described herein.This term also encompass the nucleid acids encoding AMIGO polypeptidesincluding fusion proteins, synthetic polypeptides, and fragments ofnaturally ocurring proteins, as well as derivatives thereof, asdescribed herein.

The methods can optionally be practiced in combination with contactingthe neuronal cells or nerves with other agents capable of promotingneuron survivals growth, differentiation or regeneration.

The discovery that AMIGO proteins described herein can promote neuriteoutgrowth, provides agents for use in improving nerve regeneration orpromoting nerve survival, in treating peripheral nerve injury and spinalcord injury, and in stimulation of growth of endogenous, implanted ortransplanted CNS tissue.

The present invention therefore also provides a method of promotingregeneration of an injured or severed nerve or nerve tissue, orpromoting neurite outgrowth in neuronal cells under a variety ofneurological conditions requiring neuronal cell outgrowth. The methodcomprises contacting a neuronal cell capable of extending neurites, oran injured or severed nerve, with a cell culture system comprising asubstrate containing a neurite outgrowth-promoting polypeptide of thisinvention in an amount effective to promote neurite outgrowth. Themethod may be carried out in vitro or in vivo.

The polypeptides and nucleic acids used in the present method can be anyof the subject polypeptides described herein.

Any of a variety of mammalian neuronal cells can be treated by thepresent method in the cell culture system, including neuronal cells frombrain, CNS, peripheral nerves and the like. In addition, the cells canbe from any of a variety of mammalian species, including human, mouse,chicken, and any other mammalian species, including the agriculturalstock and non-domesticated mammals.

In selecting a particular subject polypeptide for use in the methods,any of the polypeptides described herein can be utilized to promoteneurite outgrowth, irrespective of the species of neuronal cell andspecies of AMIGO protein from which a subject polypeptide is derived.However, it is preferred to use a human AMIGO protein to induce neuriteoutgrowth on a human neuronal cell, and the like species selectivity.Thus, in preferred embodiments, the method uses rat neuronal cells and apolypeptide derived from a rat AMIGO protein, or human neuronal cellsand a polypeptide derived from a human AMIGO protein, or mouse neuronalcells and a polypeptide derived from a mouse AMIGO protein, etc.

The neurite outgrowth-promoting composition can be attached to thesubstrate, can be contacted in the liquid phase or in a collagen gelphase. Depending on the assay system used, the AMIGO protein may promoteoutgrowth when bound onto the solid surfaces but may inhibit theneuronal outgrowth when provided in liqued phase. The composition maycontain the subject polypeptide in the form of a fusion protein asdescribed herein. The method may be practiced using the subjectpolypeptide in any of the various apparati format described herein.

The invention also provides methods and compositions for identifyingagents which modulate the interaction of AMIGO with AMIGO, EpiethelialGrowth Factor Receptor or AMIGO ligand (AMIGO ligand may be selectedfrom the group of binding partner, endogenous, exogenous protein orsubstance capable of binding to AMIGO) and for modulating theseinteractions. The methods for identifying AMIGO modulators findparticular application in commercial drug screens. These methodsgenerally comprise (1) combining an AMIGO polypeptide, an AMIGO, EGFR orligand polypeptide and a candidate agent under conditions whereby, butfor the presence of the agent, the AMIGO and AMIGO/EGFR/AMIGO ligandpolypeptides engage in a first interaction, and (2) determining a secondinteraction of the AMIGO and AMIGO/EGFR/AMIGO ligand polypeptides in thepresence of the agent, wherein a difference between the first and secondinteractions indicates that the agent modulates the interaction of theAMIGO and AMIGO/EGFR/AMIGO ligand polypeptides.

The subject methods of modulating the interaction of AMIGO involvecombining an AMIGO polypeptide, an AMIGO/EGFR/AMIGO ligand polypeptideand a modulator under conditions whereby, but for the presence of themodulator, the AMIGO and AMIGO/EGFR/AMIGO ligand polypeptides engage ina first interaction, whereby the AMIGO and AMIGO/EGFR/AMIGO ligandpolypeptides engage in a second interaction different from the firstinteraction. In a particular embodiment, the modulator is dominantnegative form of the AMIGO, EGFR or AMIGO ligand polypeptide.

In one embodiment, the present invention provides AMIGO compounds thatbind to epidermal growth factor receptor (EGFR), as well as compositionscontaining one or a combination of such compounds. The AMIGO compoundspreferably inhibit (e.g., block) binding of EGFR ligands, such as EGFand TGF-.alpha., to EGFR or even more preferably inhibit thephosphorylation of EGFR. For example, binding of EGFR ligand to EGFRand/or EGFR phosphorylation can be inhibited by at least about 10%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% and preferably results in theprevention of EGFR-mediated cell signaling.

In one embodiment exemplified herein, AMIGO compounds of the inventionare AMIGO DNA constructs having an AMIGO cDNA cloned into a vector.Other AMIGO compounds are also encompassed by the invention, includingAMIGO peptides, variants, biologically active fragments, an antigenicfragment of AMIGO, anti-AMIGO antibodies or binding portion thereof andand nucleic acids encoding said polypeptides that have retained theirbinding and/or EGFR phosphorylation inhibiting characteristics. Theantibodies can be whole antibodies or antigen-binding fragments of theantibodies, including Fab, F(ab′).sub.2, Fv and chain Fv fragments.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A and 1B. Cloning of AMIGO as an amphoterin-induced gene inhippocampal neurons. (1A) Analysis of ordered differential display ongel electrophoresis, from which the band corresponding to AMIGO was cutfor sequencing (marked with arrow). Lane 1, sample from amphoterinmatrix; lane 2, sample from laminin matrix. (1B) AMIGO induction wasconfirmed by using RT-PCR. Lane 1 contains an RT-PCR reaction fromhippocampal neurons on amphoterin and lane 2 on laminin. Glyceraldehyde3-phosphate dehydrogenase (GAPDH) was analysed as a control.

FIGS. 2A and 2B. Primary structure of human AMIGO, AMIGO2 and AMIGO3.(2A) Alingment of the three AMIGOs (SEQ ID NOS: 2, 4, and 6) where theidentical amino acids between the all AMIGOs are highlighted in red withwhite letters and similar amino acids are highlighted in red with blackletters. Different domains found in the AMIGOs are marked with colouredboxes above the sequences. (2B) Schematic view of the three AMIGOs.

FIG. 3. RT-PCR mRNA analysis of AMIGO, AMIGO2 and AMIGO3 in differentadult mouse tissues. GAPDH, glyceraldehyde 3-phosphate dehydrogenase.

FIGS. 4A, 4B and 4C. In situ hybridization analysis of AMIGO mRNA. InE13 mouse embryo the AMIGO mRNA expression is highest in the dorsal rootganglia (DRG in 4A and 4B) and in the trigeminal ganglion (TG in 4A).(4C) In the adult mouse cerebrum the AMIGO expression is highest in thehippocampal formation where the most intense signal is seen in thedentate gyrus (DG). The pyramidal cell layers CA1-CA3 also expressAMIGO.

FIGS. 5A and 5B. Characterization of the recombinant AMIGO Ig-fusionprotein and of anti-AMIGO antibodies. (5A) The recombinant AMIGOIg-fusion protein (lanes 1, 3 and 5) and protein lysates from adultbrain (lanes 2, 4 and 6) were silver stained (lanes 1 and 2) orimmunoblotted with rabbit anti-AMIGO antibodies (lanes 3-6). Anti-AMIGOidentifies both the AMIGO Ig-fusion protein (lane 3) and one 65 kD bandin rat brain lysate (lane 4). Binding of the antibodies to the bandcorresponding to AMIGO was inhibited by the peptide used forimmunization (5A, lanes 5 and 6). Tissue sections were also inhibited ina dose-dependent manner by the peptide (shown for theimmunohistochemistry of the adult cerebellum in 5B).

FIG. 6. AMIGO expression displays a dual character during braindevelopment. Western blotting of AMIGO using crude brain extracts fromdifferent developmental stages reveals clear AMIGO expression during thelate embryonic (E) and perinatal development, starting at the E14 stage.The AMIGO expression is downregulated during postnatal (P) stagesP6-P10. The expression is again upregulated between the stages P10 andP12 and remains high in the adult brain. The upregulation coincides withthe onset of myelination as demonstrated by the comparison with theCNPase expression. The expression of AMIGO and CNPase display a parallelincrease during postnatal development. W; postnatal week.

FIGS. 7A, 7B, 7C, 7D, 7E and 7F. AMIGO is localized to axonal fibertracts in tissue and in cultured cells. Immunohistochemical staining ofrat tissues revealed that AMIGO is specifically expressed in the nervoussystem. In E15 embryo (7A) immunostaining is observed in developingfiber tracts and nerves, like in the ventral part of the marginal layer(ml) of the spinal cord (SC) and in the nerves connecting to the dorsalroot ganglion (DRG) and to the spinal cord. In the adult animal (7B, 7C,7D and 7E) AMIGO is also detected in nerve fibers. In the cerebellum(7B) the most intense staining is detected in fibers on both sides ofthe granule cell layer (G), as in the characteristic basket-likestructure (arrow) formed by the basket cell axons around the Purkinjecell soma (p). Fibers in the cerebellar white matter (W) are alsostained. In general, myelinated fiber tracts are clearly stained inadult animals as demonstrated by the similar staining of AMIGO (panel7C) and CNPase (panel 7D) around the hippocampus in sagittal sections.In addition to the cerebellar basket cell axons, non-myelinated fibersare also stained in hippocampus (panel 7C, higher magnification in panel7E). These CNPase negative fibers of the hippocampus reside in thevicinity of the CA3 pyramidal cell bodies. In cultured hippocampalneurons (panel 7F) AMIGO is also detected in neuronal processes byimmunofluorescence staining. G, granule cell layer of the cerebellarcortex; M; molecular layer of the cerebellar cortex; CA1, CA1 region;CA3, CA3 region; h, hilus. Scale bar 50 μm in panels 7A, 7B, 7E and 7F;500 μm in panels 7C and 7D.

FIGS. 8A, 8B, 8C and 8D. AMIGO promotes neurite outgrowth of hippocampalneurons.

(8A) Substratum coated with 25 μg/ml of AMIGO promotes neurite outgrowthof E18 hippocampal neurons. (8B) Cells on the control substratum coatedwith 25 μg/ml of the Fc protein without the AMIGO ectodomain is shownfor comparison. (8C) AMIGO induced hippocampal neurite outgrowth after24 h of culture. The AMIGO Ig-fusion (gray bars) and the Fc controlprotein (black bars) were coated as follows; 0 μg/ml (1), 3.125 μg/ml(2), 6.25 μg/ml (3), 12.5 μg/ml (4), 25 μg/ml (5), 50 μg/ml (6), 100μg/ml (7). (8D) AMIGO-induced neurite outgrowth (the substratum coatedwith 25 μg/ml of the AMIGO Ig-fusion protein) is blocked by the AMIGOIg-fusion protein in the assay medium. The AMIGO Ig-fusion (gray bars)and the Fc control protein (black bars) were added into the culturemedium as follows; 0 μg/ml (1), 3.125 μg/ml (2), 6.25 μg/ml (3), 12.5μg/ml (4), 25 μg/ml (5), 50 μg/ml (6), 100 μg/ml (7). The error barsgive the standard deviation calculated from 15 microscopy fields inthree independent experiments. Scale bar 50 μm in panels 8A and 8B.

FIGS. 9A, 9B, and 9C. Soluble AMIGO inhibits fasciculation inhippocampal neurons. (9A) E18 hippocampal neurons on poly-L-lysinesubstratum with 25 μg/ml of the AMIGO Ig-fusion in the culture medium.(9B) E18 hippocampal neurons on poly-L-lysine substratum with 25 μg/mlthe Fc control protein is shown for comparison. (9C) Total length ofprocesses, the diameter of which is <2 μm (formed from 1-3 neurites) onpoly-L-lysine substratum. The AMIGO Ig-fusion and (gray bars) and the Fccontrol protein (black bars) were added into the culture medium asfollows; 0 μg/ml (white bar)(1), 3.125 μg/ml (2), 6.25 μg/ml (3), 12.5μg/ml (4), 25 μg/ml (5). The error bars in panel 9C give the standarddeviation calculated from 12 microscopy fields in three independentexperiments. Scale bar 50 μm in panel 9A and 9B.

FIGS. 10A, 10B, 10C, and 10D. Homophilic interaction of AMIGO. (10A)Co-immunoprecipitation experiment. Lane 1, cells transfected withfull-length GFP-tagged AMIGO and full-length V5-tagged AMIGO; lane 2,full length GFP-tagged AMIGO and soluble V5-tagged AMIGO; lane 3,transfected only with full-length GFP-tagged AMIGO; lane 4, full lengthGFP-tagged AMIGO and full-length V5-tagged human RAGE. Full lengthGFP-tagged AMIGO was co-immunoprecipitated with full length V5-taggedAMIGO (lane 1) and by using soluble V5-tagged AMIGO containing only theectodomain (lane 2) Co-immunoprecipitation could be also shown byprecipitating with GFP antibody. (10B) Kinetics of bead aggregation.N_(t) and N₀ are the total number of particles at incubation times t and0 respectively. The extent of bead aggregation is represented by theindex N_(t)/N₀. Gray bars represent AMIGO Ig-fusion coated beads andblack bars Fc coated beads. (10C-10D) Bead aggregation after 60 minusing protein A beads coated with the AMIGO Ig-fusion (10C) or with theFc control (10D). The error bars give the standard deviation calculatedfrom 12 microscopy fields in three independent experiments.

FIG. 11. Multiple alignment for the leucine-rich repeat areas of Slit1,Nogo-receptor and AMIGO (SEQ ID NOS: 33-39). The identical amino acidsbetween Slit1 and Nogo-receptor compared to the AMIGO are highlighted inblack and similar amino acids are highlighted in gray. The consensussequence of the 6 LRR motifs of the AMIGO are shown above the sequences.

FIG. 12. The three dimensional structure of the immunoglobulin domain,schematic presentation. Ig-domain is a sandwich of two antiparallel betasheets. (Principles of Biochemistry, Horton et al. 2002)

FIGS. 13A and 13B. Structure of ribonuclease inhibitor. 13A) Ribbondiagram of the structure of porcine RI generated using the programMOLSCRIPT. 13B) Consensus sequences (SEQ ID NOS: 40-41) and secondarystructure of LRRs of porcine RI. The sequence of RI was aligned so thattwo types of repeats (A and B) alternate in the sequence. One-letteramino acid code is used. ‘x’ indicates any amino acid and ‘a’ denotes analiphatic amino acid. The part of the repeat that is strongly conservedin all LRR proteins is underlined, and the conserved residues are shownin bold. Below the sequence, solid lines mark the core region ofIg-sheet and helix; dots denote extensions of helix in differentrepeats. (Kobe and Deisenhofer 1995)

FIG. 14. Structure of RNase A-RI complex. In the ribbon diagram, RNase Ais dark and RI is light. (Kobe and Deisenhofer 1995)

FIG. 15. Schematic drawings of the structures of some LRR-containingproteins. Tartan is a protein involved in Drosophila development (Changet al. 1993, Milan et al. 2001). Slit protein contains additionaldomains, which are not represented here. Sig, signal peptide; AFR, aminoterminal flanking region; LRR, leucine-rich repeat; CFR, carboxyterminal flanking region; PI, phosphatidylinositol. (Hayata et al. 1998)

FIG. 16. Schematic presentation of the predicted structure of AMIGO.

FIG. 17. Specificity of AMIGO staining in tissue. α-AMI (anti-AMIGOantibody) was incubated with rising concentrations of AMIP2 or AMIP1peptide. Tissue sections from rat cerebellum were stained with peptideincubated antibody. Increasing concentration of AMIP2 peptide decreasesand finally blocks the tissue staining completely. Evidently, thebinding of α-AMI to tissue sections is inhibited by AMIP2 peptide.Control peptide AMIP1 does not have an effect on α-AMI binding even inhigh concentrations.

FIG. 18. Coronal section of the rat cerebrum stained with α-AMI.Myelinated fiber tracts are clearly stained. Some areas of the cerebralcortex are stained and one of them is marked with arrowhead (same areasare also stained with the oligodendrocyte marker α-CNPase and withα-NF-M). Non-myelinated structures are stained in the CA3 region of thehippocampus (arrow).

FIGS. 19A and 19B. Coronal section of the hippocampal CA3 region (arrowin FIG. 7, higher magnification). 19A) staining with α-AMI 19B) stainingwith α-NF-M. Both stainings are located near the proximal part of theapical dendrites of the pyramidal cells. This layer is called stratumlucidum. Less intensively stained round structures are the cell nucleistained with hematoxylin. Scale bar 25 μm.

FIGS. 20A, 20B, 20C, and 20D. Sagittal sections of the rat hippocampus.20 a) staining with α-AMI 20 b) staining with α-CNPase. Both antibodiesstain the myelinated nerve fibers in and around the hippocampus. Inaddition, α-AMI causes strong staining of non-myelinated structures inthe CA3 region of the hippocampus and in the hilus (h) of the dentategyrus (DG). 20 c) and 20 d) Higher magnification of staining with α-AMI.The staining of the CA3 region and of the dentate gyrus has a fiber-likestructure (arrows). Scale bar 50 μm.

FIGS. 21A and 21B. Higher magnification of the cerebral cortex. 21 a)staining with α-AMI 21 b) staining with α-NF-M. Same areas of thecerebral cortex are stained both with α-AMI and with α-NF-M. In closerexamination, some of the thick apical dendrites of the pyramidal cells(arrows) and some thin fibers (arrowheads) are stained with bothantibodies. Cell soma and basal dendrites of pyramidal cells are alsostained with α-NF-M. Scale bar 50 μm.

FIGS. 22A and 22B. Cerebellar sections stained with α-AMI. 22 a) Coronalsection of the cerebellum. Cerebellar cortex consists of three layers:outermost molecular layer (M), Purkinje cell layer (P) and granule celllayer (G). White matter (W) underlies the cerebellar cortex. α-AMIappears to stain myelinated fibers in the white matter and in thegranule cell layer. The basket-like structure (arrow) formed by thebasket cell axons around the Purkinje cell soma (p) and fibers in themolecular layer are also stained. In the molecular layer the staining isrestricted to the inner part of the layer and stained fibers mainly runparallel to Purkinje cell layer. 22 b) Sagittal section of thecerebellum. In the medial part of the cerbellum, the structure of thestaining in white matter (W) resembles a string of pearls. Scale bar 25μm.

FIGS. 23A, 23B, and 23C. Transverse section of the spinal cord whitematter. 23 a) staining with α-AMI 23 b) staining with α-CNPase 23 c)staining with α-NF-M. Clear, round areas of the section are the myelinsheaths. Small spots (arrow) are clearly stained inside the myelinsheath with α-AMI and with α-NF-M. These spots seem to be thetransections of axons. They are not stained with α-CNPase. The axontracts running parallel to the section plane are stained with α-NF-M butnot with α-AMI. Scale bar 50 μm.

FIGS. 24A and 24B. Immunohistochemistry of the kidney. Staining withα-AMI (24 a) or with α-NF-M (24 b) detects the same small structures inthe kidney (arrows). Consequently, α-AMI staining is located in thenerves of the kidney. Scale bar 100 μm.

FIGS. 25A, 25B, 25C, and 25D. Immunohistochemistry of the head of 18 dayold embryo. Staining with α-AMI detects developing fiber tracts andcranial nerves, like the optic nerve (in panel 25 a) and the internalcapsule (in panel 25 c). Staining in retina (arrow in panel 25 a) islocated in the nerve fiber layer. Nerve fiber layer consist of ganglioncell axons, which form the optic nerve. Control sections (panel 25 b and25 d) are stained with AMIP2 blocked α-AMI. Scale bar 100 μm.

FIGS. 26A and 26B. Western blotting of AMIGO using crude rat brainextracts from different developmental stages. Same total weight oftissue was used from each sample. Brains of 16- and 18-day old embryo(E16 and E18), of 1-, 2-, 4-, 6-, 8-, 10- and 14-day old rat (P1-P14)and of adult rat were used. AMIGOIg fusion protein (AMIIg) was used as acontrol sample. In panel 26 a) Western blot is detected with α-AMI andα-CNPase. α-AMI detects about 65 kDa protein band and weaker proteinband, about 130 kDa. α-CNPase detects about 48 kDa protein band. TheAMIGO expression displays dual character during brain development.Immunoblotting reveals clear AMIGO expression during the late embryonic(E) and perinatal development. The AMIGO expression is downregulatedduring postnatal (P) stages P4-P10. The expression is again upregulatedbetween stages P10 and P14 and remains high in the adult brain. Theupregulation coincides with the onset of myelination as demonstrated bythe comparison with the CNPase expression. The expression of AMIGO andCNPase display a parallel increase during postnatal development. Inpanel 26 b) Western blot is stained with Ponceau stain to compare thetotal amount of protein in each sample.

FIG. 27. Coimmunoprecipitation of AMIGOs with EGFR. Stable EGFRexpressing 293 cells were transfected with V5-tagged full length AMIGO(lane1), EC-part containing AMIGO (lane 2), full length AMIGO2 (lane 3)or with full length AMIGO3 (lane 4). The coimmunoprecipitations weredone by using anti-EGFR antibodies and the detection was done by usinganti-V5 antibodies. The result shows that both AMIGO and AMIGO2 bind theEGFR and only the EC-part is enough for the binding (shown for theAMIGO).

FIG. 28. Homo- and heterophilic binding of AMIGO, AMIGO2 and AMIGO3.Coimmunoprecipitation was done by using anti-V5-tag antibodies and thedetection was done by using anti-GFP-tag antibodies. Lanes 1-5 containsfull length AMIGO with GFP-tag; lanes 6-9 contains full length AMIGO2with GFP-tag; lanes 10-12 full length AMIGO3 with GFP-tag. V5-taggedproteins used in this experiment: AMIGO full length in lane 1; AMIGOEC-part in lane 2; AMIGO2 full length in lanes 3 and 6; AMIGO2 EC-partin lane 7; AMIGO3 full length in lanes 4, 8 and 10; AMIGO3 EC-part inlane 11; RAGE full length in lanes 5, 9 and 12. Pictures shows that fulllength AMIGO-GFP could be co-immunoprecipitated with full length AMIGO,AMIGO2 and AMIGO3 but not with full length RAGE. Full length AMIGO-GFPcould also be coimmunoprecipitated with only EC-part containing AMIGO.The full length AMIGO2-GFP could be coimmunoprecipitated with fulllength AMIGO2 and AMIGO3 but also with only EC-part containing AMIGO2.The full length AMIGO3-GFP could be coimmunoprecipitated with fulllength AMIGO3 and only EC-part containing AMIGO3. Thecoimmunoprecipitation results show that AMIGOs could bind each others inheterophilically but they also posses homophilic binding properties.

FIG. 29. AMIGO inhibits EGFR phosphorylation. When AMIGO and flag-taggedhuman EGFR are expressed together in HEK293T cells AMIGO clearlyinhibits the EGFR autophosphorylation induced by EGF ligation whencompared to AMIGO2, AMIGO3 and vector control.

DETAILED DESCRIPTION OF THE INVENTION

Amphoterin and laminin are both neurite outgrowth-promoting factors. Thegenes induced on amphoterin matrix were detected by using the ordereddifferential display method (Matz et al., 1997) from hippocampalneurons, which were cultured on amphoterin or laminin matrix. A novelgene was seen to be induced on amphoterin. The whole coding sequence forthis differentially expressed gene was cloned and named as AMIGO(AMphoterin Induced Gene and Orphan receptor). The predicted amino acidsequences of the AMIGO codes type I transmembrane protein containing asignal sequence for secretion and a transmembrane domain. The deducedextracellular part of the AMIGO contains six leucine-rich repeats (LRRs)flanked by cysteine-rich LRRN- and LRRC-terminal domains and oneimmunoglobulin domain close to the transmembrane region. The deduced 100amino acid long cytosolic part of the protein do not contain any knowndomains. We have also identified a novel family of transmembraneproteins consisting of AMIGO, AMIGO2 and AMIGO3. These three proteinsshow clear homology with each other; their length and location ofdifferent domains are highly identical (FIG. 2 B).

Based on RT-PCR experiments, in situ hybridization andimmunohistochemistry, AMIGO is an essentially nervous system specificprotein. One cellular mechanism in the growth of axonal connections isfasciculation: axons grow along each other by using pioneer axons as thesubstratum for the growth cones of the later ones. Interestingly, adominant negative approach using AMIGO ectodomain in the culture mediumclearly suggests a role for AMIGO in fasciculation. Further, AMIGOdisplays a homophilic binding mechanism that would explain its role infasciculation. It is also noteworthy that the LRR sequences of theAMIGOs display homology with the slit proteins and with the Nogoreceptor (FIG. 11) that have been implicated in axon growth,regeneration and guidance. The second upregulation of the AMIGOexpression suggests a role in myelination. It seems reasonable thatAMIGO would mediate cell-to-cell interactions also at this stage ofdevelopment. Further, AMIGO expression remains high until adulthood.This suggests that AMIGO plays a role in regeneration and plasticity ofthe adult fiber tracts, the mechanisms of which commonly recapitulatemechanisms of fiber tract development.

Thus, this invention is based on the discovery and characterization of anovel human gene/protein termed AMIGO and its homologous counterpartsdesignated as AMIGO2 and AMIGO3. Together these three proteins form anovel family of transmembrane proteins (for simplicity, all of theseproteins are hereinafter referred as AMIGO or AMIGOs).

In one embodiment, the invention provides a purified protein comprising,or alternatively consisting of a polypeptide, a biologically activefragment, or an antigenic fragment of AMIGO.

In another embodiment the present invention is directed to proteinswhich comprise, or alternatively consist of, an amino acid sequencewhich is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100%,identical to AMIGO protein.

Due to the degeneracy of the genetic code, one of ordinary skill in theart will immediately recognize that a large number of the nucleic acidmolecules having a sequence at least 80%, 85%, 90%, 95%, 96%, 97%, 98%,99%, or 100% identical to the nucleic acid sequence of the cDNAcontained in SEQ ID NO:1, 3, or 5 or fragments thereof, will encodepolypeptides “having functional activity.” In fact, since degeneratevariants of any of these nucleotide sequences all encode the samepolypeptide, in many instances, this will be clear to the skilledartisan. It will be further recognized in the art that, for such nucleicacid molecules that are not degenerate variants, a reasonable numberwill also encode a polypeptide having functional activity. This isbecause the skilled artisan is fully aware of amino acid substitutionsthat are either less likely or not likely to significantly effectprotein function (e.g. replacing one aliphatic amino acid with a secondaliphatic amino acid), as further described below.

For example, guidance concerning how to make phenotypically silent aminoacid substitutions is provided in Bowie et al., “Deciphering the Messagein Protein Sequences: Tolerance to Amino Acid Substitutions,” Science247:1306-1310 (1990), wherein the authors indicate that there are twomain strategies for studying the tolerance of an amino acid sequence tobe changed.

The first strategy exploits the tolerance of amino acid substitutions bynatural selection during the process of evolution. By comparing aminoacid sequences in different species, conserved amino acids can beidentified. These conserved amino acids are likely important for proteinfunction. In contrast, the amino acid positions where substitutions havebeen tolerated by natural selection indicates that these positions arenot critical for protein function. Thus, positions tolerating amino acidsubstitution could be modified while still maintaining biologicalactivity of the protein.

In addition to naturally occurring allelic variants of AMIGO, changescan be introduced by mutation into AMIGO sequences that incuralterations in the amino acid sequences of the encoded AMIGOpolypeptide. Nucleotide substitutions leading to amino acidsubstitutions at “non-essential” amino acid residues can be made in thesequence of an AMIGO polypeptide. A “non-essential” amino acid residueis a residue that can be altered from the wild-type sequences of AMIGOwithout altering its biological activity, whereas an “essential” aminoacid residue is required for such biological activity. For example,amino acid residues that are conserved among the AMIGO molecules of theinvention are predicted to be particularly non-amenable to alteration.Amino acids for which conservative substitutions can be made are wellknown in the art. Useful conservative substitutions are shown in TableB, “Preferred substitutions.” Conservative substitutions whereby anamino acid of one class is replaced with another amino acid of the sametype fall within the scope of the subject invention so long as thesubstitution does not materially alter the biological activity of thecompound.

The second strategy uses genetic engineering to introduce amino acidchanges at specific positions of a cloned gene to identify regionscritical for protein function. For example, site directed mutagenesis oralanine-scanning mutagenesis (introduction of single alanine mutationsat every residue in the molecule) could be used. See Cunningham et al.,Science 244:1081-1085 (1989). The resulting mutant molecules can then betested for biological activity. Besides conservative amino acidsubstitutions (See Table B below), variants of the present inventioninclude (i) substitutions with one or more of the non-conserved aminoacid residues, where the substituted amino acid residues may or may notbe one encoded by the genetic code, or (ii) substitutions with one ormore of the amino acid residues having a substituent group, or (iii)fusion of the mature polypeptide with another compound, such as acompound to increase the stability and/or solubility of the polypeptide(for example, 8961 polyethylene glycol), or (iv) fusion of thepolypeptide with additional amino acids, such as, for example, an IgG Fcfusion peptide, serum albumin (preferably human serum albumin) or afragment or variant thereof, or leader or secretory sequence, or asequence facilitating purification. Such variant polypeptides are deemedto be within the scope of those skilled in the art from the teachingsherein. TABLE B Preferred substitutions Original Exemplary Preferredresidue substitutions substitutions Ala (A) Val, Leu, Ile Val Arg (R)Lys, Gln, Asn Lys Asn (N) Gln, His, Lys, Arg Gln Asp (D) Glu Glu Cys (C)Ser Ser Gln (Q) Asn Asn Glu (E) Asp Asp Gly (G) Pro, Ala Ala His (H)Asn, Gln, Lys, Arg Arg Ile (I) Leu, Val, Met, Ala, Leu Phe, NorleucineLeu (L) Norleucine, Ile, Ile Val, Met, Ala, Phe Lys (K) Arg, Gln, AsnArg Met (M) Leu, Phe, Ile Leu Phe (F) Leu, Val, Ile, Ala, Leu Tyr Pro(P) Ala Ala Ser (S) Thr Thr Thr (T) Ser Ser Trp (W) Tyr, Phe Tyr Tyr (Y)Trp, Phe, Thr, Ser Phe Val (V) Ile, Leu, Met, Phe, Leu Ala, Norleucine

A further embodiment of the invention relates to polypeptides whichcomprise the amino acid sequence of a polypeptide having an amino acidsequence which contains at least one amino acid substitution, but notmore than 50 amino acid substitutions, even more preferably, not morethan 40 amino acid substitutions, still more preferably, not more than30 amino acid substitutions, and still even more preferably, not morethan 20 amino acid substitutions from a polypeptide sequence disclosedherein. It is highly preferable for a polypeptide to have an amino acidsequence which comprises the amino acid sequence of a polypeptide, aportion, or a complement of SEQ ID NO:2, 4 or 6 in order ofever-increasing preference, at least one, but not more than 10, 9, 8, 7,6, 5, 4, 3, 2 or 1 amino acid substitutions.

In preferred embodiments, the amino acid substitutions are conservative.

In specific embodiments, the polypeptides of the invention comprise, oralternatively, consist of, fragments or variants of a reference aminoacid sequence encoded by SEQ ID NO:2, 4 or 6 wherein the fragments orvariants have 1-5, 5-10, 5-25, 5-50, 10-50 or 50-150, amino acid residueadditions, substitutions, and/or deletions when compared to thereference amino acid sequence.

In one embodiment techniques suitable for the production of AMIGOpolypeptide are well known in the art and include isolating AMIGO froman endogenous source of the polypeptide, peptide synthesis (using apeptide synthesizer) and recombinant techniques (or any combination ofthese techniques).

In one embodiment, the isolated nucleic acid molecule comprises anucleotide sequence encoding a protein, wherein the protein comprises anamino acid sequence at least about 45%, preferably 60%, more preferably70%, 80%, 90%, and most preferably about 95% homologous to that of anAMIGO.

In another embodiment, AMIGO polypeptide variants have at least (I)about 80% amino acid sequence identity with a full-length native AMIGOpolypeptide sequence shown in SEQ ID NO:2, 4 or 6 (2) an AMIGOpolypeptide sequence lacking the signal peptide, (3) any other fragmentof a full-length AMIGO polypeptide sequence. For example, AMIGOpolypeptide variants include AMIGO polypeptides wherein one or moreamino acid residues are added or deleted at the N- or C-terminus of thefull-length native amino acid sequence. An AMIGO polypeptide variantwill have at least about 80% amino acid sequence identity, preferably atleast about 81% amino acid sequence identity, more preferably at leastabout 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98% amino acid sequence identity and most preferably atleast about 99% amino acid sequence identity with a full-length nativesequence AMIGO polypeptide sequence. An AMIGO polypeptide variant mayhave a sequence lacking the signal peptide or any other fragment of afull-length AMIGO polypeptide sequence. Ordinarily, AMIGO variantpolypeptides are at least about 10 amino acids in length, often at leastabout 20 amino acids in length, more often at least about 30, 40, 50,60, 70, 80, 90, 100 or 150 amino acids in length, or more.

One aspect of the invention provides an isolated nucleic acid moleculecomprising, or alternatively consisting of, a polynucleotide having anucleotide sequence selected from the group consisting of (a) anucleotide sequence described in SEQ ID NO:1, 3 or 5 (b) a nucleotidesequence in SEQ ID NO:1, 3 or 5 part of which encodes a mature AMIGOpolypeptide; (c) a nucleotide sequence which encodes a biologicallyactive fragment of an AMIGO polypeptide; (d) a nucleotide sequence whichencodes an antigenic fragment of an AMIGO polypeptide; (e) a nucleotidesequence complementary to any of the nucleotide sequences in (a), (b),(c), (d), above.

The invention further encompasses nucleic acid molecules that differfrom the nucleotide sequences due to degeneracy of the genetic code andthus encode the same AMIGO protein as shown in sequence of SEQ ID NO:2,4 or 6.

In addition sequence polymorphisms that change the amino acid sequencesof the AMIGO may exist within a population. For example, allelicvariation among individuals will exhibit genetic polymorphism in AMIGO.The terms “gene” and “recombinant gene” refer to nucleic acid moleculescomprising an open reading frame (ORF) encoding AMIGO, preferably avertebrate AMIGO. Such natural allelic variations can typically resultin 1-5% variance in AMIGO. Any and all such nucleotide variations andresulting amino acid polymorphisms in the AMIGO, which are the result ofnatural allelic variation and that do not alter the functional activityof the AMIGO are within the scope of the invention.

Moreover, AMIGO from other species that have a nucleotide sequence thatdiffers from the human sequence of AMIGO are contemplated. Nucleic acidmolecules corresponding to natural allelic variants and homologues ofAMIGO cDNAs of the invention can be isolated based on their homology toAMIGO using cDNA-derived probes to hybridize to homologous AMIGOsequences under stringent conditions.

“AMIGO variant polynucleotide” or “AMIGO variant nucleic acid sequence”means a nucleic acid molecule which encodes an active AMIGO that (1) hasat least about 80% nucleic acid sequence identity with a nucleotide acidsequence encoding a full-length native AMIGO, (2) a full-length nativeAMIGO lacking the signal peptide, or (3) any other fragment of afull-length AMIGO. Ordinarily, an AMIGO variant polynucleotide will haveat least about 80% nucleic acid sequence identity, more preferably atleast about 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98% nucleic acid sequence identity and yet morepreferably at least about 99% nucleic acid sequence identity with thenucleic acid sequence encoding a full-length native AMIGO. An AMIGOvariant polynucleotide may encode full-length native AMIGO lacking thesignal peptide with or without the signal sequence, or any otherfragment of a full-length AMIGO. Variants do not encompass the nativenucleotide sequence.

Ordinarily, AMIGO variant polynucleotides are at least about 30nucleotides in length, often at least about 60, 90, 120, 150, 180, 210,240, 270, 300, 400 nucleotides in length, more often at least about 500nucleotides in length, or more.

The structure and sequence of the mammalian AMIGO cDNA sequence whichencodes the mouse and human sequences disclosed herein, make it possibleto clone gene sequences from other mammals which encode the AMIGO. Ofparticular interest to the present invention is the ability to clone thehuman AMIGO molecules using the sequences disclosed herein. The DNAencoding AMIGO may be obtained from any cDNA library prepared fromtissue believed to possess the AMIGO mRNA and to express it at adetectable level, as shown herein in the Examples. Accordingly, AMIGODNA can be conveniently obtained from a cDNA library prepared, forexample, from mammalian fetal liver, brain, muscle, intestine, andperipheral nerves. The AMIGO-encoding gene may also be obtained from agenomic library or by oligonucleotide synthesis.

Libraries are screened with probes (such as antibodies to the AMIGO oroligonucleotides of about 20-80 bases) designed to identify the gene ofinterest or the protein encoded by it. Screening the cDNA or genomiclibrary with the selected probe may be conducted using standardprocedures as described in chapters 10-12 of Sambrook et al., MolecularCloning: A Laboratory Manual (New York: Cold Spring Harbor LaboratoryPress, 1989) or alternatively to use PCR methodology as described insection 14 of Sambrook et al., supra.

Amino acid sequence variants of AMIGO are prepared by introducingappropriate nucleotide changes into the AMIGO DNA, or by synthesis ofthe desired AMIGO polypeptide. Such variants represent insertions,substitutions, and/or specified deletions of, residues within or at oneor both of the ends of the amino acid sequence of a naturally occurringAMIGO with sequence of SEQ ID NO:2, 4 or 6. Preferably, these variantsrepresent insertions and/or substitutions within or at one or both endsof the mature sequence, and/or insertions, substitutions and/orspecified deletions within or at one or both of the ends of the signalsequence of the AMIGO. Any combination of insertion, substitution,and/or specified deletion is made to arrive at the final construct,provided that the final construct possesses the desired biologicalactivity as defined herein.

Variations in the native sequence as described above can be made usingany of the techniques and guidelines for conservative andnon-conservative mutations set forth in U.S. Pat. No. 5,364,934. Theseinclude oligonucleotide-mediated (site-directed) mutagenesis, alaninescanning, and PCR mutagenesis.

The nucleic acid (e.g., cDNA or genomic DNA) encoding the AMIGO isinserted into a replicable vector for further cloning (amplification ofthe DNA) or for expression. Many vectors are available. The vectorcomponents generally include, but are not limited to, one or more of thefollowing: a signal sequence, an origin of replication, one or moremarker genes, an enhancer element, a promoter, and a transcriptiontermination sequence.

The AMIGOs of this invention may be produced recombinantly not onlydirectly, but also as a fusion polypeptide with a heterologouspolypeptide, which is preferably a signal sequence or other polypeptidehaving a specific cleavage site at the N-terminus of the mature proteinor polypeptide. Fusion proteins can be easily created using recombinantmethods. A nucleic acid encoding AMIGO can be fused in-frame with anon-AMIGO encoding nucleic acid, to the AMIGO N- or COOH-terminus, orinternally. Fusion genes may also be synthesized by conventionaltechniques, including automated DNA synthesizers. An AMIGO fusionprotein may include any portion to the entire AMIGO, including anynumber of the biologically active portions. Fusion polypeptides areuseful in expression studies, cell-localization, bioassays, and AMIGOpurification

Alternatively, AMIGO fusion protein can also be easily created using PCRamplification and anchor primers that give rise to complementaryoverhangs between two consecutive gene fragments that can subsequentlybe annealed and reamplified to generate a chimeric gene sequence(Ausubel et al., supra).

The signal sequence may be a component of the vector, or it may be apart of the AMIGO DNA that is inserted into the vector. The heterologoussignal sequence selected preferably is one that is recognized andprocessed (i.e., cleaved by a signal peptidase) by the host cell. Forprokaryotic host cells that do not recognize and process the nativeAMIGO signal sequence, the signal sequence is substituted by aprokaryotic signal sequence selected, for example, from the group of thealkaline phosphatase, penicillinase, or heat-stable enterotoxin IIleaders. For yeast secretion the native signal sequence may besubstituted by, e.g., the yeast invertase leader, alpha-factor leader(including Saccharomyces and Kluyveromyces, alpha-factor leaders, thelatter described in U.S. Pat. No. 5,010,182 issued Apr. 23, 1991), oracid phosphatase leader, the Candida albicans glucoamylase leader (EP362,179 published Apr. 4, 1990). In mammalian cell expression the nativesignal sequence (e.g., the AMIGO presequence that normally directssecretion of AMIGO from human cells in vivo) is satisfactory, althoughother mammalian signal sequences may be suitable, such as signalsequences from other animal AMIGOs, and signal sequences from secretedpolypeptides of the same or related species, as well as viral secretoryleaders, for example, the herpes simplex gD signal.

Expression and cloning vectors usually contain a promoter that isrecognized by the host organism and is operably linked to the AMIGOnucleic acid. Vector choice is dictated by the organism or cells beingused and the desired fate of the vector. Vectors may replicate once inthe target cells, or may be “suicide” vectors. In general, vectorscomprise signal sequences, origins of replication, marker genes,enhancer elements, promoters, and transcription termination sequences.The choice of these elements depends on the organisms in which thevector will be used and are easily determined. Some of these elementsmay be conditional, such as an inducible or conditional promoter that isturned “on” when conditions are appropriate.

Vectors can be divided into two general classes: Cloning vectors arereplicating plasmid or phage with regions that are non-essential forpropagation in an appropriate host cell, and into which foreign DNA canbe inserted; the foreign DNA is replicated and propagated as if it werea component of the vector. An expression vector (such as a plasmid,yeast, or animal virus genome) is used to introduce foreign geneticmaterial into a host cell or tissue in order to transcribe and translatethe foreign DNA. In expression vectors, the introduced DNA is operablylinked to elements, such as promoters, that signal to the host cell totranscribe the inserted DNA. Some promoters are exceptionally useful,such as inducible promoters that control gene transcription in responseto specific factors. Operably linking AMIGO or anti-sense construct toan inducible promoter can control the expression of AMIGO or fragments,or anti-sense constructs. Examples of classic inducible promotersinclude those that are responsive to a-interferon, heat-shock, heavymetal ions, and steroids such as glucocorticoids (Kaufman R J, VectorsUsed for Expression in Mammalian Cells,” Methods in Enzymology, GeneExpression Technology, David V. Goeddel, ed., 1990, 185:487-511) andtetracycline. Other desirable inducible promoters include those that arenot endogenous to the cells in which the construct is being introduced,but, however, is responsive in those cells when the induction agent isexogenously supplied.

Promoters are untranslated sequences located upstream (5′) to the startcodon of a structural gene (generally within about 100 to 1000 bp) thatcontrol the transcription and translation of particular nucleic acidsequence, such as the AMIGO nucleic acid sequence, to which they areoperably linked. Such promoters typically fall into two classes,inducible and constitutive. Inducible promoters are promoters thatinitiate increased levels of transcription from DNA under their controlin response to some change in culture conditions, e.g., the presence orabsence of a nutrient or a change in temperature. At this time a largenumber of promoters recognized by a variety of potential host cells arewell known. These promoters are operably linked to AMIGO-encoding DNA byremoving the promoter from the source DNA by restriction enzymedigestion and inserting the isolated promoter sequence into the vector.Both the native AMIGO promoter sequence and many heterologous promotersmay be used to direct amplification and/or expression of the AMIGO DNA.However, heterologous promoters are preferred, as they generally permitgreater transcription and higher yields of AMIGO as compared to thenative AMIGO promoter. Various promoters exist for use with prokaryotic,eukaryotic, yeast and mammalian host cells, known for skilled artisan.

Expression vectors used in eukaryotic host cells (yeast, fungi, insect,plant, animal, human, or nucleated cells from other multicellularorganisms) will also contain sequences necessary for the termination oftranscription and for stabilizing the mRNA. Such sequences are commonlyavailable from the 5′ and, occasionally 3′, untranslated regions ofeukaryotic or viral DNAs or cDNAs. These regions contain nucleotidesegments transcribed as polyadenylated fragments in the untranslatedportion of the mRNA encoding AMIGO.

Construction of suitable vectors containing one or more of theabove-listed components employs standard ligation techniques. Isolatedplasmids or DNA fragments are cleaved, tailored, and religated in theform desired to generate the plasmids required.

Particularly useful in the practice of this invention are expressionvectors that provide for the transient expression in mammalian cells ofDNA encoding AMIGO. In general, transient expression involves the use ofan expression vector that is able to replicate efficiently in a hostcell, such that the host cell accumulates many copies of the expressionvector and, in turn, synthesizes high levels of a desired polypeptideencoded by the expression vector, Sambrook et al., supra, pp.16.17-16.22. Transient expression systems, comprising a suitableexpression vector and a host cell, allow for the convenient positiveidentification of polypeptides encoded by cloned DNAs, as well as forthe rapid screening of such polypeptides for desired biological orphysiological properties. Thus, transient expression systems areparticularly useful in the invention for purposes of identifying analogsand variants of AMIGO that are biologically active.

Propagation of vertebrate cells in culture (tissue culture) has become aroutine procedure. See, e.g., Tissue Culture, Academic Press, Kruse andPatterson, editors (1973). Examples of useful mammalian host cell linesare monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651);Chinese hamster ovary cells/-DHFR (CHO, Urlaub et al., Proc. Natl. Acad.Sci USA, 77:4216 (1980)); human cervical carcinoma cells (HELA, ATCC CCL2); and canine kidney cells (MDCK, ATCC CCL 34);

Host cells are transfected and preferably transformed with theabove-described expression or cloning vectors for AMIGO production andcultured in conventional nutrient media modified as appropriate forinducing promoters, selecting transformants, or amplifying the genesencoding the desired sequences.

Transfection refers to the taking up of an expression vector by a hostcell whether or not any coding sequences are in fact expressed. Numerousmethods of transfection are known to the ordinarily skilled artisan, forexample, electroporation. Successful transfection is generallyrecognized when any indication of the operation of this vector occurswithin the host cell.

Transformation means introducing DNA into an organism so that the DNA isreplicable, either as an extrachromosomal element or by chromosomalintegrant. Depending on the host cell used, transformation is done usingstandard techniques appropriate to such cells. The calcium treatmentemploying calcium chloride, as described in section 1.82 of Sambrook etal., supra, or electroporation is generally used for prokaryotes orother cells that contain substantial cell-wall barriers.

General aspects of mammalian cell host system transformations have beendescribed in U.S. Pat. No. 4,399,216 issued Aug. 16, 1983.Transformations into yeast are typically carried out according to themethod of Van Solingen et al., J. Bact., 130:946 (1977) and Hsiao etal., Proc. Natl. Acad. Sci. USA, 76:3829 (1979). However, other methodsfor introducing DNA into cells, such as by nuclear microinjection,electroporation, bacterial protoplast fusion with intact cells, orpolycations, e.g., polybrene, polyomithine, etc., may also be used. Forvarious techniques for transforming mammalian cells, see Keown et al.,Methods in Enzymology, 185:527-537 (1990) and Mansour et al., Nature,336:348-352 (1988).

Prokaryotic cells used to produce the AMIGO polypeptide of thisinvention are cultured in suitable media as described generally inSambrook et al., supra. In general, principles, protocols, and practicaltechniques for maximizing the productivity of mammalian cell culturescan be found in Mammalian Cell Biotechnology: a Practical Approach, M.Butler, ed. (IRL Press, 1991).

Gene amplification and/or expression may be measured in a sampledirectly, for example, by conventional Southern blotting, Northernblotting to quantitate the transcription of mRNA (Thomas, Proc. Natl.Acad. Sci. USA, 77:5201-5205 (1980)), dot blotting (DNA analysis), or insitu hybridization, using an appropriately labeled probe, based on thesequences provided herein. Various labels may be employed, most commonlyradioisotopes, particularly ³²P. However, other techniques may also beemployed, such as using biotin-modified nucleotides for introductioninto a polynucleotide or antibodies recognizing specific duplexes,including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes orDNA-protein duplexes.

Gene expression, alternatively, can be measured by immunologicalmethods, such as immunohistochemical staining of tissue sections andassay of cell culture or body fluids, to quantitate directly theexpression of gene product. With immunohistochemical stainingtechniques, a cell sample is prepared, typically by dehydration andfixation, followed by reaction with labeled antibodies specific for thegene product coupled, where the labels are usually visually detectable,such as enzymatic labels, fluorescent labels, luminescent labels, andthe like. A particularly sensitive staining technique suitable for usein the present invention is described by Hsu et al., Am. J. Clin. Path.,75:734-738 (1980).

Recombinant Production

When AMIGO is produced in a recombinant cell other than one of humanorigin, the AMIGO is completely free of proteins or polypeptides ofhuman origin. However, it is necessary to purify AMIGO from recombinantcell proteins or polypeptides to obtain preparations that aresubstantially homogeneous as to AMIGO. As a first step, the culturemedium or lysate can be centrifuged to remove particulate cell debris.AMIGO can then be purified from contaminant soluble proteins andpolypeptides with the following procedures, which are exemplary ofsuitable purification procedures: by fractionation on an ion-exchangecolumn; ethanol precipitation; reverse phase HPLC; chromatography onsilica; chromatofocusing; immunoaffinity; epitope-tag binding resin;SDS-PAGE; ammonium sulfate precipitation; gel filtration using, forexample, Sephadex G-75; and protein A Sepharose columns to removecontaminants such as IgG.

AMIGO variants in which residues have been deleted, inserted, orsubstituted are recovered in the same fashion as native sequence AMIGO,taking account of any substantial changes in properties occasioned bythe variation. Immunoaffinity resins, such as a monoclonal anti-AMIGOresin, can be employed to absorb the AMIGO variant by binding it to atleast one remaining epitope.

Variants can be assayed as taught herein. A change in the immunologicalcharacter of the AMIGO molecule, such as affinity for a given antibody,can be measured by a competitive-type immunoassay. Other potentialmodifications of protein or polypeptide properties such as redox orthermal stability, hydrophobicity, susceptibility to proteolyticdegradation, or the tendency to aggregate with carriers or intomultimers are assayed by methods well known in the art.

This invention encompasses chimeric polypeptides comprising AMIGO fusedto a heterologous polypeptide. A chimeric AMIGO is one type of AMIGOvariant as defined herein. In one preferred embodiment, the chimericpolypeptide comprises a fusion of the AMIGO with a tag polypeptide whichprovides an epitope to which an anti-tag antibody or molecule canselectively bind. The epitope-tag is generally provided at the amino- orcarboxyl-terminus of the AMIGO. Such epitope-tagged forms of the AMIGOare desirable, as the presence thereof can be detected using a labeledantibody against the tag polypeptide. Also, provision of the epitope tagenables the AMIGO to be readily purified by affinity purification usingthe anti-tag antibody. Affinity purification techniques and diagnosticassays involving antibodies are described later herein.

Tag polypeptides and their respective antibodies are well known in theart. Examples include the flu HA tag polypeptide and its antibody 12CA5(Field et al., Mol. Cell. Biol., 8:2159-2165 (1988)); the c-myc tag andthe 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto (Evan et al.,Molecular and Cellular Biology, 5:3610-3616 (1985)); and the HerpesSimplex virus glycoprotein D (gD) tag and its antibody (Paborsky et al.,Protein Engineering, 3(6):547-553 (1990)). Other tag polypeptides havebeen disclosed. Examples include the Flag-peptide (Hopp et al.,BioTechnology, 6:1204-1210 (1988)); the KT3 epitope peptide (Martin etal., Science, 255:192-194 (1992)); an alpha-tubulin epitope peptide(Skinner et al., J. Biol. Chem., 266:15163-15166 (1991)); and the T7gene protein peptide tag (Lutz-Freyermuth et al., Proc. Natl. Acad. Sci.USA, 87:6393-6397 (1990)).

Once the tag polypeptide has been selected, an antibody thereto can begenerated using the techniques disclosed herein. A C-terminalpoly-histidine sequence tag is preferred. Poly-histidine sequences allowisolation of the tagged protein by Ni-NTA chromatography as described(Lindsay et al. Neuron 17:571-574 (1996)), for example.

The general methods suitable for the construction and production ofepitope-tagged AMIGO are the same as those disclosed hereinabove.

Epitope-tagged AMIGO can be conveniently purified by affinitychromatography using the anti-tag antibody. The matrix to which theaffinity antibody is attached is most often agarose, but other matricesare available (e.g. controlled pore glass orpoly(styrenedivinyl)benzene). The epitope-tagged AMIGO can be elutedfrom the affinity column by varying the buffer pH or ionic strength oradding chaotropic agents, for example.

Chimeras constructed from an AMIGO sequence linked to an appropriateimmunoglobulin constant domain sequence (immunoadhesins) are known inthe art. Immunoadhesins reported in the literature include fusions ofthe T cell receptor (Gascoigne et al., Proc. Natl. Acad. Sci. USA, 84:2936-2940 (1987)); CD4* (Capon et al., Nature 337: 525-531 (1989);Traunecker et al., Nature, 339: 68-70 (1989); Zettmeissl et al., DNACell Biol USA, 9: 347-353 (1990); Byrn et al., Nature, 344: 667-670(1990)); TNF receptor (Ashkenazi et al., Proc. Natl. Acad. Sci. USA, 88:10535-10539 (1991); Lesslauer et al., Eur. J. Immunol., 27: 2883-2886(1991); Peppel et al., J. Exp. Med., 174:1483-1489 (1991)); and IgEreceptor alpha* (Ridgway et al., J. Cell. Biol., 115:abstr. 1448(1991)), where the asterisk (*) indicates that the receptor is member ofthe immunoglobulin superfamily.

The simplest and most straightforward immunoadhesin design combines thebinding region(s) of the “adhesin” protein with the hinge and Fc regionsof an immunoglobulin heavy chain. Ordinarily, when preparing theAMIGO-immunoglobulin chimeras of the present invention, nucleic acidencoding the AMIGO will be fused C-terminally to nucleic acid encodingthe N-terminus of an immunoglobulin constant domain sequence, howeverN-terminal fusions are also possible.

Typically, in such fusions the encoded chimeric polypeptide will retainat least functionally active hinge and CH2 and CH3 domains of theconstant region of an immunoglobulin heavy chain. Fusions are also madeto the C-terminus of the Fc portion of a constant domain, or immediatelyN-terminal to the CH1 of the heavy chain or the corresponding region ofthe light chain.

The precise site at which the fusion is made is not critical; particularsites are well known and may be selected in order to optimise thebiological activity, secretion or binding characteristics of theAMIGO-immunoglobulin chimeras.

The choice of host cell line for the expression of AMIGO immunoadhesinsdepends mainly on the expression vector. Another consideration is theamount of protein that is required. Milligram quantities often can beproduced by transient transfections utilizing, for example, calciumphosphate or DEAE-dextran method (Aruffo et al., Cell, 61:1303-1313(1990); Zettmeissl et al., DNA Cell Biol. US, 9:347-353 (1990)). Iflarger amounts of protein are desired, the immunoadhesin can beexpressed after stable transfection of a host cell line, for example,introducing the expression vectors into Chinese hamster ovary (CHO)cells in the presence of an additional plasmid encoding dihydrofolatereductase.

Antibodies

AMIGO nucleic acid is useful for the preparation of AMIGO polypeptide byrecombinant techniques exemplified herein which can then be used forproduction of anti-AMIGO antibodies having various utilities describedbelow.

Antibodies useful for immunohistochemical staining and/or assay ofsample fluids may be either monoclonal or polyclonal.

The invention further includes an antibody that specifically binds withAMIGO, or a fragment thereof. In a preferred embodiment, the inventionincludes an antibody that inhibits the biological activity of AMIGO. Theantibody is useful for the identification for AMIGO in a diagnosticassay for the determination of the levels of AMIGO in a mammal having adisease associated with AMIGO levels. In addition, an antibody thatspecifically binds AMIGO is useful for blocking the interaction betweenAMIGO and its receptor, and is therefore useful in a therapeutic settingfor treatment of AMIGO related disease, as described herein.

Monoclonal antibodies directed against full length or peptide fragmentsof an AMIGO protein or peptide may be prepared using any well-knownmonoclonal antibody preparation procedures, such as those described, forexample, in Harlow et al. (1988, In: Antibodies, A Laboratory Manual,Cold Spring Harbor, N.Y.). Anti-AMIGO mAbs may be prepared usinghybridoma methods comprising at least four steps: (1) immunizing a host,or lymphocytes from a host; (2) harvesting the mAb secreting (orpotentially secreting) lymphocytes, (3) fusing the lymphocytes toimmortalized cells, and (4) selecting those cells that secrete thedesired (anti-AMIGO) mAb. The mAbs may be isolated or purified from theculture medium or ascites fluid by conventional Ig purificationprocedures such as protein A-Sepharose, hydroxylapatite chromatography,gel electrophoresis, dialysis, ammonium sulfate precipitation oraffinity chromatography (Harlow et al, supra).

A mouse, rat, guinea pig, hamster, or other appropriate host isimmunized to elicit lymphocytes that produce or are capable of producingAbs that will specifically bind to the immunogen. Alternatively, thelymphocytes may be immunized in vitro.

If human cells are desired, peripheral blood lymphocytes are generallyused; however, spleen cells or lymphocytes from other mammalian sourcesare preferred.

The immunogen typically includes AMIGO or an AMIGO fusion protein.

The invention further comprises humanized and human anti-AMIGO Abs.

Humanized forms of non-human Abs are chimeric Igs, Ig chains orfragments (such as Fv, Fab, Fab′, F(ab′) or other antigen-bindingsubsequences of Abs) that contain minimal sequence derived fromnon-human Ig.

Generally, a humanized antibody has one or more amino acid residuesintroduced from a non-human source. These non-human amino acid residuesare often referred to as “import” residues, which are typically takenfrom an “import” variable domain. Humanization is accomplished bysubstituting rodent CDRs or CDR sequences for the correspondingsequences of a human antibody (Jones et al., Nature 321:522-525 (1986);Riechmann et al., Nature 332:323-327 (1988); Verhoeyen et al., Science239:1534-1536, (1988). Such “humanized” Abs are chimeric Abs (U.S. Pat.No. 4,816,567, 1989), wherein substantially less than an intact humanvariable domain has been substituted by the corresponding sequence froma non-human species. In practice, humanized Abs are typically human Absin which some CDR residues and possibly some FR residues are substitutedby residues from analogous sites in rodent Abs. Humanized Abs includehuman Igs (recipient antibody) in which residues from a complementarydetermining region (CDR) of the recipient are replaced by residues froma CDR of a non-human species (donor antibody) such as mouse, rat orrabbit, having the desired specificity, affinity and capacity. In someinstances, corresponding non-human residues replace Fv frameworkresidues of the human Ig. Humanized Abs may comprise residues that arefound neither in the recipient antibody nor in the imported CDR orframework sequences. In general, the humanized antibody comprisessubstantially all of at least one, and typically two, variable domains,in which most if not all of the CDR regions correspond to those of anon-human Ig and most if not all of the FR regions are those of a humanIg consensus sequence. The humanized antibody optimally also comprisesat least a portion of an Ig constant region typically that of a human Ig(Jones et al., supra; Presta L G, Curr Opin Biotechnol 3:394-398 (1992).

Human Abs can also be produced using various techniques, including phagedisplay libraries (Hoogenboom et al., Nucleic Acids Res 19:4133-4137(1991); Marks et al., Biotechnology (NY) 10:779-83 (1991) and thepreparation of human mAbs (Boemer et al., J Immunol 147(1):86-95 (1991);Reisfeld and Sell, Monoclonal Antibodies and Cancer Therapy Alan R.Liss, Inc., New York (1985). Similarly, introducing human Ig genes intotransgenic animals in which the endogenous Ig genes have been partiallyor completely inactivated can be exploited to synthesize human Abs. Uponchallenge, human antibody production is observed, which closelyresembles that seen in humans in all respects, including generearrangement, assembly, and antibody repertoire (U.S. Pat. No.5,545,807, 1996; U.S. Pat. No. 5,545,806, 1996; U.S. Pat. No. 5,569,825,1996; U.S. Pat. No. 5,633,425, 1997; U.S. Pat. No. 5,661,016, 1997; U.S.Pat. No. 5,625,126, 1997; Fishwild et al., Nat Biotechnol 14:845-51(1996); Lonberg and Huszar, Int Rev Immunol 13:65-93 (1995); Lonberg etal., Nature 368:856-9 (1994); Marks et al., Biotechnology (NY)10:779-783 (1992)).

In one preferred embodiment the instant inventions also comprisesbi-specific mAbs that are monoclonal, preferably human or humanized,that have binding specificities for at least two different antigens. Forexample, a binding specificity is AMIGO; the other is for any antigen ofchoice, preferably a cell surface protein or receptor or receptorsubunit.

Traditionally, the recombinant production of bi-specific Abs is based onthe co-expression of two Ig heavy-chain/light-chain pairs, where the twoheavy chains have different specificities (Milstein and Cuello, Nature305:537-540 (1983)). Because of the random assortment of Ig heavy andlight chains, the resulting hybridomas (quadromas) produce a potentialmixture of ten different antibody molecules, of which only one has thedesired bi-specific structure. The desired antibody can be purifiedusing affinity chromatography or other techniques (WO 93/08829, (1993);Traunecker et al., Trends Biotechnol 9:109-113 (1991)).

To manufacture a bi-specific antibody (Suresh et al., Methods Enzymol.121:210-228 (1986)), variable domains with the desired antibody-antigencombining sites are fused to Ig constant domain sequences. The fusion ispreferably with an Ig heavy-chain constant domain, comprising at leastpart of the hinge, CH2, and CH3 regions. Preferably, the firstheavy-chain constant region (CH1) containing the site necessary forlight-chain binding is in at least one of the fusions. DNAs encoding theIg heavy-chain fusions and, if desired, the Ig light chain, are insertedinto separate expression vectors and are co-transfected into a suitablehost organism.

Fab fragments may be directly recovered from E. coli and chemicallycoupled to form bi-specific Abs. For example, fully humanizedbi-specific F(ab′) Abs can be produced (Shalaby et al., J Exp Med.175:217-225 (1992)). Each Fab fragment is separately secreted from E.coli and directly coupled chemically in vitro, forming the bi-specificantibody.

Various techniques for making and isolating bi-specific antibodyfragments directly from recombinant cell culture have also beendescribed. For example, leucine zipper motifs can be exploited (Kostelnyet al., Immunol. 148:1547-1553 (1992)). Peptides from the Fos and Junproteins are linked to the Fab portions of two different Abs by genefusion. The antibody homodimers are reduced at the hinge region to formmonomers and then reoxidized to form antibody heterodimers. This methodcan also produce antibody homodimers.

The “diabody” technology (Holliger et al., Proc Natl Acad Sci USA.90:6444-6448 (1993)) provides an alternative method to generatebi-specific antibody fragments. The fragments comprise a heavy-chainvariable domain (VH) connected to a light-chain variable domain (VL) bya linker that is too short to allow pairing between the two domains onthe same chain. The VH and VL domains of one fragment are forced to pairwith the complementary VL and VH domains of another fragment, formingtwo antigen-binding sites. Another strategy for making bi-specificantibody fragments is the use of single-chain Fv (sFv) dimers (Gruber etal., Immunol. 152:5368-5374 (1994)). Abs with more than two valenciesare also contemplated, such as tri-specific Abs (Tutt et al., J.Immunol. 147:60-69 (1991)).

Polyclonal Abs can be raised in a mammalian host, for example, by one ormore injections of an immunogen and, if desired, an adjuvant. Typically,the immunogen and/or adjuvant are injected in the mammal by multiplesubcutaneous or intraperitoneal injections. The immunogen may includeAMIGO or an AMIGO fusion protein.

Examples of adjuvants include Freund's complete and monophosphoryl LipidA synthetic-trehalose dicorynomycolate (MPL-TDM). To improve the immuneresponse, an immunogen may be conjugated to a protein that isimmunogenic in the AMIGO host, such as keyhole limpet hemocyanin (KLH),serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor.Protocols for antibody production are described by (Harlow et al,supra). Alternatively, pAbs may be made in chickens, producing IgYmolecules (Schade et al, The production of avian (egg yolg) antibodies:IgY. The report and recommendations of ECVAM workshop. Alternatives toLaboratory Animals NAILA). 24:925-934 (1996)).

Treatment

The AMIGO protein, AMIGO gene, and AMIGO nucleic acids are believed tofind ex vivo or in vivo therapeutic use for administration to a mammal,particularly humans, in the treatment of diseases or disorders, relatedto AMIGO activity or benefited by AMIGO-responsiveness. Particularlypreferred are neurologic disorders, preferably central nervous systemdisorders, Parkinson's disease, Alzheimer's disease, neuronal trauma orbrain tumor.

The patient is administered an effective amount of AMIGO protein,biologically active peptide fragment, or variant of the invention ornucleic acids encoding said peptides. Therapeutic methods comprisingadministering AMIGO, AMIGO agonists, AMIGO antagonists or anti-AMIGOantibodies are within the scope of the present invention. The presentinvention also provides for pharmaceutical compositions comprising AMIGOprotein, peptide fragment, or derivative in a suitable pharmacologicalcarrier. The AMIGO protein, peptide fragment, or variant may beadministered systemically or locally.

A disease or medical disorder is considered to be nerve damage if thesurvival or function of nerve cells and/or their axonal processes iscompromised. Such nerve damage occurs as the result conditions including(a) Physical injury, which causes the degeneration of the axonalprocesses and/or nerve cell bodies near the site of the injury; (b)Ischemia, as a stroke; (c) Exposure to neurotoxins, such as the cancerand AIDS chemotherapeutic agents such as cisplatin and dideoxycytidine(ddC), respectively; (d) Chronic metabolic diseases, such as diabetes orrenal dysfunction; and (e) Neurodegenerative diseases such asParkinson's disease, Alzheimer's disease, and Amyotrophic LateralSclerosis (ALS), which cause the degeneration of specific neuronalpopulations. Conditions involving nerve damage include Parkinson'sdisease, Alzheimer's disease, Amyotrophic Lateral Sclerosis, stroke,diabetic polyneuropathy, toxic neuropathy, glial scar, and physicaldamage to the nervous system such as that caused by physical injury ofthe brain and spinal cord or crush or cut injuries to the arm and handor other parts of the body, including temporary or permanent cessationof blood flow to parts of the nervous system, as in stroke.

The invention features a method for treating a mammal who has sufferedan injury to the central nervous system, such as stroke or a traumaticinjury. The method involves administering an AMIGO protein, peptidefragment, or variant of the invention to the affected mammal at leastsix hours after onset of the injury; for example twelve, twenty-four,forty-eight hours, or even longer following injury. No practical endpoint the therapeutic window in which the invention can be practiced hasyet been established. The invention can be used to treat one or moreadverse consequences of central nervous system injury that arise from avariety of conditions. Thrombus, embolus, and systemic hypotension areamong the most common causes of stroke. Other injuries may be caused byhypertension, hypertensive cerebral vascular disease, rupture of ananeurysm, an angioma, blood dyscrasia, cardiac failure, cardiac arrest,cardiogenic shock, kidney failure, septic shock, head trauma, spinalcord trauma, seizure, bleeding from a tumor, or other loss of bloodvolume or pressure. These injuries lead to disruption of physiologicfunction, subsequent death of neurons, and necrosis (infarction) of theaffected areas. The term “stroke” connotes the resulting sudden anddramatic neurologic deficits associated with any of the foregoinginjuries.

The terms “ischemia” or “ischemic episode,” as used herein, mean anycircumstance that results in a deficient supply of blood to a tissue.Thus, a central nervous system ischemic episode results from aninsufficiency or interruption in the blood supply to any locus of thebrain such as, but not limited to, a locus of the cerebrum, cerebellumor brain stem. The spinal cord, which is also a part of the centralnervous system, is equally susceptible to ischemia resulting fromdiminished blood flow. An ischemic episode may be caused by aconstriction or obstruction of a blood vessel, as occurs in the case ofa thrombus or embolus. Alternatively, the ischemic episode may resultfrom any form of compromised cardiac function, including cardiac arrest,as described above. Where the deficiency is sufficiently severe andprolonged, it can lead to disruption of physiologic function, subsequentdeath of neurons, and necrosis (infarction) of the affected areas. Theextent and type of neurologic abnormality resulting from the injurydepend on the location and size of the infarct or the focus of ischemia.Where the ischemia is associated with a stroke, it can be either globalor focal in extent.

It is expected that the invention will also be useful for treatingtraumatic injuries to the central nervous system that are caused bymechanical forces, such as a blow to the head. Trauma can involve atissue insult selected from abrasion, incision, contusion, puncture,compression, etc., such as can arise from traumatic contact of a foreignobject with any locus of or appurtenant to the mammalian head, neck orvertebral column. Other forms of traumatic injury can arise fromconstriction or compression of mammalian CNS tissue by an inappropriateaccumulation of fluid (e.g., a blockade or dysfunction of normalcerebrospinal fluid or vitreous humor fluid production, turnover orvolume regulation, or a subdural or intracranial hematoma or edema).Similarly, traumatic constriction or compression can arise from thepresence of a mass of abnormal tissue, such as a metastatic or primarytumor.

It is expected that the invention will also be useful for treatingtumors or metastatic tumor cells, especially brain tumors. The mostcommon brain tumors are gliomas, which begin in the glial tissue.Astrocytomas arise from small, star-shaped cells called astrocytes. Inadults, astrocytomas most often arise in the cerebrum. A grade IIIastrocytoma is sometimes called anaplastic astrocytoma. A grade IVastrocytoma is usually called glioblastoma multiforme. Brain stemgliomas occur in the lowest, stemlike part of the brain. The brain stemcontrols many vital functions. Most brain stem gliomas are high-gradeastrocytomas. Ependymomas usually develop in the lining of theventricles. They may also occur in the spinal cord. Oligodendrogliomasarise in the cells that produce myelin, the fatty covering that protectsnerves. These tumors usually arise in the cerebrum. They grow slowly andusually do not spread into surrounding brain tissue. Medulloblastomasdevelop from primitive nerve cells that normally do not remain in thebody after birth. For this reason, medulloblastomas are sometimes calledprimitive neuroectodermal tumors (PNET). Most medulloblastomas arise inthe cerebellum; however, they may occur in other areas as well.Meningiomas grow from the meninges. They are usually benign. Becausethese tumors grow very slowly, the brain may be able to adjust to theirpresence; meningiomas often grow quite large before they cause symptoms.They occur most often in women between 30 and 50 years of age.Schwannomas are benign tumors that begin in Schwann cells, which producethe myelin that protects the acoustic nerve. Acoustic neuromas are atype of schwannoma. Craniopharyngiomas develop in the region of thepituitary gland near the hypothalamus. They are usually benign; however,they are sometimes considered malignant because they can press on ordamage the hypothalamus and affect vital functions. Germ cell tumorsarise from primitive (developing) sex cells, or germ cells. The mostfrequent type of germ cell tumor in the brain is the germinoma. Pinealregion tumors occur in or around the pineal gland. The tumor can be slowgrowing pineocytoma or fast growing (pineoblastoma). The pineal regionis very difficult to reach, and these tumors often cannot be removed.Treatment for a brain tumor depends on a number of factors. Among theseare the type, location, and size of the tumor, as well as the patient'sage and general health. Normally brain tumors are treated with surgery,radiation therapy, and chemotherapy. Preferred tumours amenable forAMIGO treatment express EGFR and are responsive to AMIGO mediatedinhibition of EGFR phosphorylation.

The invention is suitable for the treatment of any primate, preferably ahigher primate such as a human. In addition, however, the invention maybe employed in the treatment of domesticated mammals which aremaintained as human companions (e.g., dogs, cats, horses), which havesignificant commercial value (e.g., goats, pigs, sheep, cattle, sportingor draft animals), which have significant scientific value (e.g.,captive or free specimens of endangered species, or inbred or engineeredanimal strains), or which otherwise have value. One of ordinary skill inthe medical or veterinary arts is trained to recognize whether a mammalis afflicted with an ischemic or traumatic injury of the central nervoussystem. For example, routine testing and/or clinical or veterinarydiagnostic evaluation will reveal whether the mammal has acquired animpairment or loss of central nervous system (e.g., neurologic)function. Clinical and non-clinical indications, as well as accumulatedexperience, relating to the presently disclosed and other methods oftreatment, should appropriately inform the skilled practitioner indeciding whether a given individual is afflicted with an ischemic ortraumatic injury of the central nervous system and whether anyparticular treatment is best suited to the subject's needs, includingtreatment according to the present invention.

In gene therapy applications, genes are introduced into cells in orderto achieve in vivo synthesis of a therapeutically effective geneticproduct, for example for replacement of a defective gene. “Gene therapy”includes both conventional gene therapy where a lasting effect isachieved by a single treatment, and the administration of genetherapeutic agents, which involves the one time or repeatedadministration of a therapeutically effective DNA or mRNA. AntisenseRNAs and DNAs can be used as therapeutic agents for blocking theexpression of certain genes in vivo. It has already been shown thatshort antisense oligonucleotides can be imported into cells where theyact as inhibitors, despite their low intracellular concentrations causedby their restricted uptake by the cell membrane. (Zamecnik et al., Proc.Natl. Acad. Sci. USA, 83:41434146 (1986)). The oligonucleotides can bemodified to enhance their uptake, e.g., by substituting their negativelycharged phosphodiester groups by uncharged groups.

Another technique for inhibiting the expression of a gene involves theuse of RNA for induction of RNA interference (RNAi), using doublestranded (dsRNA) (Fire et al., Nature 391: 806-811. 1998) orshort-interfering RNA (siRNA) sequences (Yu et al., Proc Natl Acad SciUSA. 99:6047-52. 2002). “RNAi” is the process by which dsRNA induceshomology-dependent degradation of complimentary mRNA. In one embodiment,a synthetic antisense nucleic acid molecule is hybridized bycomplementary base pairing with a “sense” ribonucleic acid to form adouble stranded RNA. The dsRNA antisense and sense nucleic acidmolecules are provided that correspond to at least about 20, 25, 50,100, 250 or 500 nucleotides or an entire AMIGO coding strand, or to onlya portion thereof. In an alternative embodiment, the siRNAs are 30nucleotides or less in length, and more preferably 21- to23-nucleotides, with characteristic 2- to 3-nucleotide 3′-overhangingends, which are generated by ribonuclease III cleavage from longerdsRNAs. (See e.g. Tuschl T. Nat Biotechnol. 20:446-48. 2002).

Intracellular transcription of small RNA molecules can be achieved bycloning the siRNA templates into RNA polymerase III (Pol III)transcription units, which normally encode the small nuclear RNA (snRNA)U6 or the human RNAse P RNA H1. Two approaches can be used to expresssiRNAs: in one embodiment, sense and antisense strands constituting thesiRNA duplex are transcribed using constructs with individual promoters(Lee, et al. Nat. Biotechnol. 20, 500-505. 2002); in an alternativeembodiment, siRNAs are expressed as stem-loop hairpin RNA structuresthat give rise to siRNAs after intracellular processing (Brummelkamp etal. Science 296:550-553. 2002) (herein incorporated by reference).

The dsRNA/siRNA is most commonly administered by annealing sense andantisense RNA strands in vitro before delivery to the organism. In analternate embodiment, RNAi may be carried out by administering sense andantisense nucleic acids of the invention in the same solution withoutannealing prior to administration, and may even be performed byadministering the nucleic acids in separate vehicles within a very closetimeframe. Nucleic acid molecules encoding fragments and variants of anAMIGO or antisense nucleic acids complementary to an AMIGO nucleic acidsequence are additionally provided.

There are a variety of techniques available for introducing nucleicacids into viable cells. The techniques vary depending upon whether thenucleic acid is transferred into cultured cells in vitro, ex vivo, or invivo in the cells of the intended host. Techniques suitable for thetransfer of nucleic acid into mammalian cells in vitro include the useof liposomes, (Nicolau and Sene, Biochim. Biophys. Acta, 721:185-190(1982); Fraley, et al., Proc. Natl. Acad. Sci. USA, 76:3348-3352 (1979);Feigner, Sci. Am., 276(6):102-6 (1997); Feigner, Hum. Gene Ther., 7(15):1791-3, (1996)), electroporation (Tur-Kaspa, et al., Mol. Cell Biol.,6:716-718, (1986); Potter, et al., Proc. Nat. Acad. Sci. USA,81:7161-7165, (1984)), direct microinjection (Harland and Weintraub, J.Cell Biol., 101:1094-1099 (1985)), cell fusion, DEAE-dextran (Gopal,Mol. Cell Biol., 5:1188-1190 (1985), the calcium phosphate precipitationmethod (Graham and Van Der Eb, Virology, 52:456-467 (1973); Chen andOkayama, Mol. Cell Biol., 7:2745-2752, (1987); Rippe, et al., Mol. CellBiol., 10:689-695 (1990), cell sonication (Fechheimer, et al., Proc.Natl. Acad. Sci. USA, 84:8463-8467 (1987)), gene bombardment using highvelocity microprojectiles (Yang, et al., Proc. Natl. Acad. Sci. USA,87:9568-9572 (1990). The currently preferred in vivo gene transfertechniques include transfection with viral (typically retroviral)vectors and viral coat protein-liposome mediated transfection (Dzau etal., Trends in Biotechnology, 11:205-210 (1993)). In some situations itis desirable to provide the nucleic acid source with an agent thattargets the target cells, such as an antibody specific for a cellsurface membrane protein or the target cell, a ligand for a receptor onthe target cell, etc. Where liposomes are employed, proteins which bindto a cell surface membrane protein associated with endocytosis may beused for targeting and/or to facilitate uptake, e.g. capsid proteins orfragments thereof tropic for a particular cell type, antibodies forproteins which undergo internalization in cycling, and proteins thattarget intracellular localization and enhance intracellular half-life.The technique of receptor-mediated endocytosis is described, forexample, by Wu et al., J. Biol. Chem., 262:4429-4432 (1987); and Wagneret al., Proc. Natl. Acad. Sci. USA, 87:3410-3414 (1990). For review ofthe currently known gene marking and gene therapy protocols see Andersonet al., Science, 256:808-813 (1992).

Any suitable vector may be used to introduce a transgene of interestinto an animal. Exemplary vectors that have been described in theliterature include replication-deficient retroviral vectors, includingbut not limited to lentivirus vectors [Kim et al., J. Virol., 72(1):811-816 (1998); Kingsman & Johnson, Scrip Magazine, October, 1998, pp.43-46.]; adenoviral (see, for example, U.S. Pat. No. 5,824,544; U.S.Pat. No. 5,707,618; U.S. Pat. No. 5,792,453; U.S. Pat. No. 5,693,509;U.S. Pat. No. 5,670,488; U.S. Pat. No. 5,585,362; Quantin et al., Proc.Natl. Acad. Sci. USA, 89: 2581-2584 (1992); Stratford-Perricadet et al.,J. Clin. Invest., 90: 626-630 (1992); and Rosenfeld et al., Cell, 68:143-155 (1992)), retroviral (see, for example, U.S. Pat. No. 5,888,502;U.S. Pat. No. 5,830,725; U.S. Pat. No. 5,770,414; U.S. Pat. No.5,686,278; U.S. Pat. No. 4,861,719), adeno-associated viral (see, forexample, U.S. Pat. No. 5,474,935; U.S. Pat. No. 5,139,941; U.S. Pat. No.5,622,856; U.S. Pat. No. 5,658,776; U.S. Pat. No. 5,773,289; U.S. Pat.No. 5,789,390; U.S. Pat. No. 5,834,441; U.S. Pat. No. 5,863,541; U.S.Pat. No. 5,851,521; U.S. Pat. No. 5,252,479; Gnatenko et al., J.Investig. Med., 45: 87-98 (1997), an adenoviral-adenoassociated viralhybrid (see, for example, U.S. Pat. No. 5,856,152) or a vaccinia viralor a herpesviral (see, for example, U.S. Pat. No. 5,879,934; U.S. Pat.No. 5,849,571; U.S. Pat. No. 5,830,727; U.S. Pat. No. 5,661,033; U.S.Pat. No. 5,328,688); Lipofectin-mediated gene transfer (BRL); liposomalvectors [See, e.g., U.S. Pat. No. 5,631,237 (Liposomes comprising Sendaivirus proteins)]; and combinations thereof. All of the foregoingdocuments are incorporated herein by reference in the entirety.Replication-deficient adenoviral vectors, adeno-associated viral vectorsand lentiviruses constitute preferred embodiments.

In embodiments employing a viral vector, preferred polynucleotidesinclude a suitable promoter and polyadenylation sequence to promoteexpression in the target tissue of interest. For many applications ofthe present invention, suitable promoters/enhancers for mammalian cellexpression include, e.g., cytomegalovirus promoter/enhancer [Lehner etal., J. Clin. Microbiol., 29:2494-2502 (1991); Boshart et al., Cell,41:521-530 (1985)]; Rous sarcoma virus promoter [Davis et al., Hum. GeneTher., 4:151 (1993)]; simian virus 40 promoter, long terminal repeat(LTR) of retroviruses, keratin 14 promoter, and α myosin heavy chainpromoter.

In a particular embodiment of the invention, the expression construct(or the peptides discussed above) may be entrapped in a liposome.Liposomes are vesicular structures characterized by a phospholipidbilayer membrane and an inner aqueous medium. Multilamellar liposomeshave multiple lipid layers separated by aqueous medium. They formspontaneously when phospholipids are suspended in an excess of aqueoussolution. The lipid components undergo self-rearrangement before theformation of closed structures and entrap water and dissolved solutesbetween the lipid bilayers (Ghosh and Bachhawat, “In Liver Diseases,Targeted Diagnosis And Therapy Using Specific Receptors And Ligands,”Wu, G., Wu, C., ed., New York: Marcel Dekker, pp. 87-104 (1991)). Theaddition of DNA to cationic liposomes causes a topological transitionfrom liposomes to optically birefringent liquid-crystalline condensedglobules (Radler, et al., Science, 275(5301):810-4, (1997)). TheseDNA-lipid complexes are potential non-viral vectors for use in genetherapy and delivery.

Also contemplated in the present invention are various commercialapproaches involving “lipofection” technology. In certain embodiments ofthe invention, the liposome may be complexed with a hemagglutinatingvirus (HVJ). This has been shown to facilitate fusion with the cellmembrane and promote cell entry of liposome-encapsulated DNA (Kaneda, etal., Science, 243:375-378 (1989)). In other embodiments, the liposomemay be complexed or employed in conjunction with nuclear nonhistonechromosomal proteins (HMG-1) (Kato, et al., J. Biol. Chem.,266:3361-3364 (1991)). In yet further embodiments, the liposome may becomplexed or employed in conjunction with both HVJ and HMG-1. In thatsuch expression constructs have been successfully employed in transferand expression of nucleic acid in vitro and in vivo, then they areapplicable for the present invention.

Other vector delivery systems that can be employed to deliver a nucleicacid encoding a therapeutic gene into cells include receptor-mediateddelivery vehicles. These take advantage of the selective uptake ofmacromolecules by receptor-mediated endocytosis in almost all eukaryoticcells. Because of the cell type-specific distribution of variousreceptors, the delivery can be highly specific (Wu and Wu (1993),supra).

In another embodiment of the invention, the expression construct maysimply consist of naked recombinant DNA or plasmids. Transfer of theconstruct may be performed by any of the methods mentioned above thatphysically or chemically permeabilize the cell membrane. This isapplicable particularly for transfer in vitro, however, it may beapplied for in vivo use as well. Dubensky, et al., Proc. Nat. Acad. Sci.USA, 81:7529-7533 (1984) successfully injected polyomavirus DNA in theform of CaPO₄ precipitates into liver and spleen of adult and newbornmice demonstrating active viral replication and acute infection.Benvenisty and Neshif, Proc. Nat. Acad. Sci. USA, 83:9551-9555 (1986)also demonstrated that direct intraperitoneal injection of CaPO₄precipitated plasmids results in expression of the transfected genes.

Another embodiment of the invention for transferring a naked DNAexpression construct into cells may involve particle bombardment. Thismethod depends on the ability to accelerate DNA coated microprojectilesto a high velocity allowing them to pierce cell membranes and entercells without killing them (Klein, et al., Nature, 327:70-73 (1987)).Several devices for accelerating small particles have been developed.One such device relies on a high voltage discharge to generate anelectrical current, which in turn provides the motive force (Yang, etal., Proc. Natl. Acad. Sci USA, 87:9568-9572 (1990)). Themicroprojectiles used have consisted of biologically inert substancessuch as tungsten or gold beads.

Those of skill in the art are aware of how to apply gene delivery to invivo and ex vivo situations. For viral vectors, one generally willprepare a viral vector stock. Depending on the type of virus and thetiter attainable, one will deliver 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸,1×10⁹, 1×10¹⁰, 1×10¹¹ or 1×10¹² infectious particles to the patient.Similar figures may be extrapolated for liposomal or other non-viralformulations by comparing relative uptake efficiencies. Formulation as apharmaceutically acceptable composition is discussed below.

Various routes are contemplated for various cell types. For practicallyany cell, tissue or organ type, systemic delivery is contemplated. Inother embodiments, a variety of direct, local and regional approachesmay be taken. For example, the cell, tissue or organ may be directlyinjected with the expression vector or protein.

In a different embodiment, ex vivo gene therapy is contemplated. In anex vivo embodiment, cells from the patient are removed and maintainedoutside the body for at least some period of time. During this period, atherapy is delivered, after which the cells are reintroduced into thepatient.

The invention also provides antagonists of AMIGO activation (e.g., AMIGOantisense nucleic acid, RNAi, neutralizing antibodies). Administrationof AMIGO antagonist to a mammal having increased or excessive levels ofendogenous AMIGO activation is contemplated, preferably in the situationwhere such increased levels of AMIGO lead to a pathological disorder.

Pharmaceutical and Therapeutical Compositions and Formulations

The AMIGO nucleic acid molecules, AMIGO polypeptides, AMIGO agonists,AMIGO antagonists and anti-AMIGO Abs (active compounds) of theinvention, and derivatives, fragments, analogs and homologs thereof, canbe incorporated into pharmaceutical compositions.

Such compositions of AMIGO are prepared for storage by mixing AMIGOnucleic acid molecule, protein, or antibody having the desired degree ofpurity with optional physiologically acceptable carriers, excipients, orstabilizers (Remington's Pharmaceutical Sciences, 16th edition, Osol,A., Ed., (1980)), in the form of lyophilized cake or aqueous solutions.Acceptable carriers, excipients, or stabilizers are non-toxic torecipients at the dosages and concentrations employed, and includebuffers such as phosphate, citrate, and other organic acids;antioxidants including ascorbic acid; low molecular weight (less thanabout 10 residues) polypeptides; proteins, such as serum albumin,gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids such as glycine, glutamine,asparagine, arginine, or lysine; monosaccharides, disaccharides, andother carbohydrates including glucose, mannose, or dextrins; chelatingagents such as EDTA; sugar alcohols such as mannitol or sorbitol;salt-forming counter-ions such as sodium; and/or non-ionic surfactantssuch as Tween, Pluronics or polyethylene glycol (PEG).

The AMIGO nucleic acid molecule, protein, agonist, antagonist orantibodies may also be entrapped in microcapsules prepared, for example,by coacervation techniques or by interfacial polymerization (forexample, hydroxymethylcellulose or gelatin-microcapsules andpoly-(methylmethacylate) microcapsules, respectively), in colloidal drugdelivery systems (for example, liposomes, albumin microspheres,microemulsions, nano-particles, and nanocapsules), or in macroemulsions.Such techniques are disclosed in Remington's Pharmaceutical Sciences,supra.

The route of AMIGO nucleic acid molecule, protein, or antibodyadministration is in accord with known methods, e.g., those routes setforth above for specific indications, as well as the general routes ofinjection or infusion by intravenous, intraperitoneal, intracerebral,intramuscular, intraocular, intrathecal, intracranial, intraspinal,intraventricular, intraarterial, or intralesional means, or sustainedrelease systems as noted below. AMIGO nucleic acid molecule, protein, orantibody is administered continuously by infusion or by bolus injection.Generally, where the disorder permits, one should formulate and dose theAMIGO nucleic acid molecule, protein, or antibody for site-specificdelivery. Administration can be continuous or periodic. Administrationcan be accomplished by a constant- or programmable-flow implantable pumpor by periodic injections. The nucleic acid molecules of the inventioncan be inserted into vectors and used as gene therapy vectors. Genetherapy vectors can be delivered to a subject by, for example,intravenous injection, local administration (Nabel and Nabel, U.S. Pat.No. 5,328,470, 1994), or by stereotactic injection (Chen et al., Proc.Natl. Acad. Sci. USA 91:3054-3057 (1994)). The pharmaceuticalpreparation of a gene therapy vector can include an acceptable diluent,or can comprise a slow release matrix in which the gene delivery vehicleis imbedded.

Alternatively, where the complete gene delivery vector can be producedintact from recombinant cells, e.g., retroviral vectors, thepharmaceutical preparation can include one or more cells that producethe gene delivery system.

Suitable examples of sustained-release preparations includesemipermeable matrices of solid hydrophobic polymers containing theprotein, which matrices are in the form of shaped articles, e.g., films,or microcapsules. Examples of sustained-release matrices includepolyesters, hydrogels as described by Langer et al., J. Biomed. Mater.Res., 15:167-277 (1981) and Langer, Chem. Tech., 12:98-105 (1982) orpolyvinylalcohol, polylactides (U.S. Pat. No. 3,773,919, EP 58,481), ornon-degradable ethylene-vinyl acetate (Langer et al., supra).

Sustained-release AMIGO compositions also include liposomally entrappedAMIGO nucleic acid molecule, protein, agonist, antagonist or antibodies.Liposomes containing AMIGO nucleic acid molecule, protein, or antibodiesare prepared by methods known per se: Epstein et al., Proc. Natl. Acad.Sci. USA, 82:3688-3692 (1985); Hwang et al., Proc. Natl. Acad. Sci. USA,77:40304034 (1980); EP 52,322; EP 36,676; EP 88,046; EP 143,949; EP142,641; U.S. Pat. Nos. 4,485,045 and 4,544,545; and EP 102,324.Ordinarily the liposomes are of the small (about 200-800 Angstroms)unilamellar type in which the lipid content is greater than about 30 mol% cholesterol, the selected proportion being adjusted for the optimalAMIGO nucleic acid molecule, protein, or antibody therapy.

While polymers such as ethylene-vinyl acetate and lactic acid-glycolicacid enable release of molecules for over 100 days, certain hydrogelsrelease proteins for shorter time periods. When encapsulated proteinsremain in the body for a long time, they may denature or aggregate as aresult of exposure to moisture at 37° C., resulting in a loss ofbiological activity and possible changes in immunogenicity. Rationalstrategies can be devised for protein stabilization depending on themechanism involved. For example, if the aggregation mechanism isdiscovered to be intermolecular S—S bond formation throughthio-disulfide interchange, stabilization may be achieved by modifyingsulfhydryl residues, lyophilizing from acidic solutions, controllingmoisture content, using appropriate additives, and developing specificpolymer matrix compositions.

Semipermeable, implantable membrane devices are useful as means fordelivering drugs in certain circumstances. For example, cells thatsecrete soluble AMIGO or express AMIGO on their cell surface, chimerasor antibodies can be encapsulated, and such devices can be implantedinto a patient. For example, into the brain of patients suffering fromParkinson's Disease, neuronal trauma or glial scar. See, U.S. Pat. No.4,892,538 of Aebischer et al.; U.S. Pat. No. 5,011,472 of Aebischer etal.; U.S. Pat. No. 5,106,627 of Aebischer et al.; PCT Application WO91/10425; PCT Application WO 91/10470; Winn et al., Exper. Neurology,113:322-329 (1991); Aebischer et al., Exper Neurology, 111:269-275(1991); and Tresco et al., ASAIO, 38:17-23 (1992).

Accordingly, also included is a method for preventing or treating damageto a nerve or damage to other AMIGO-responsive cells, which comprisesimplanting cells that secrete AMIGO or express AMIGO on their cellsurface, its agonists or antagonists as may be required for theparticular condition, into the body of patients in need thereof.Finally, the present invention includes a device for preventing ortreating nerve damage or damage to other cells as taught herein byimplantation into a patient comprising a semipermeable membrane, and acell that secretes AMIGO (or its agonists or antagonists as may berequired for the particular condition) encapsulated within said membraneand said membrane being permeable to AMIGO (or its agonists orantagonists) and impermeable to factors from the patient detrimental tothe cells. The patient's own cells, transformed to produce AMIGO exvivo, could be implanted directly into the patient, optionally withoutsuch encapsulation. The methodology for the membrane encapsulation ofliving cells is familiar to those of ordinary skill in the art, and thepreparation of the encapsulated cells and their implantation in patientsmay be accomplished without under experimentation.

The present invention includes, therefore, a method for preventing ortreating nerve damage by implanting cells, into the body of a patient inneed thereof, cells either selected for their natural ability togenerate or engineered to secrete AMIGO or AMIGO antibody. Preferably,the expressed or secreted AMIGO or antibody being soluble, human matureAMIGO when the patient is human. The implants are preferablynon-immunogenic and/or prevent immunogenic implanted cells from beingrecognized by the immune system. For CNS delivery, a preferred locationfor the implant is the cerebral spinal fluid of the spinal cord.

An effective amount of AMIGO nucleic acid molecule, protein, agonist,antagonist or antibody to be employed therapeutically will depend, forexample, upon the therapeutic objectives, the route of administration,and the condition of the patient. Accordingly, it will be necessary forthe therapist to titre the dosage and modify the route of administrationas required to obtain the optimal therapeutic effect. Typically, theclinician will administer the AMIGO protein or antibody until a dosageis reached that achieves the desired effect. A typical daily dosage forsystemic treatment might range from about 1 microgram/kg to up to 10mg/kg or more, depending on the factors mentioned above. As analternative general proposition, the AMIGO nucleic acid molecule,protein, or antibody is formulated and delivered to the target site ortissue at a dosage capable of establishing in the tissue an AMIGO levelthat is efficacious but not unduly toxic. This intra-tissueconcentration should be maintained if possible by continuous infusion,sustained release, topical application, AMIGO-expressing cell implant,or injection at empirically determined frequencies. The progress of thistherapy is easily monitored by conventional assays.

As will be appreciated by one of ordinary skill in the art, theformulated compositions contain therapeutically-effective amounts of theAMIGO protein, peptide fragment, or variant of the invention ormodulator of AMIGO receptors. That is, they contain an amount whichprovides appropriate concentrations of the agent to the affected nervoussystem tissue for a time sufficient to stimulate a detectablerestoration of central nervous system function, up to and including acomplete restoration thereof. As will be appreciated by those skilled inthe art, these concentrations will vary depending upon a number offactors, including the biological efficacy of the selected agent, thechemical characteristics (e.g., hydrophobicity) of the specific agent,the formulation thereof, including a mixture with one or moreexcipients, the administration route, and the treatment envisioned,including whether the active ingredient will be administered directlyinto a tissue site, or whether it will be administered systemically. Thepreferred dosage to be administered also is likely to depend on suchvariables such as the condition of the diseased or damaged tissues, andthe overall health status of the particular mammal. As a general matter,single, daily, biweekly or weekly dosages of 0.00001-1000 mg of an AMIGOprotein, peptide fragment, or variant of the invention or agonists ofAMIGO receptors are sufficient with 0.0001-100 mg being preferable, and0.001 to 10 mg being even more preferable. Alternatively, a single,daily, biweekly or weekly dosage of 0.01-1000.mu·g/kg body weight, morepreferably 0.01-10 mg/kg body weight, may be advantageously employed.The present effective dose can be administered in a single dose or in aplurality (two or more) of installment doses, as desired or consideredappropriate under the specific circumstances. A bolus injection ordiffusable infusion formulation can be used. If desired to facilitaterepeated or frequent infusions, implantation of a semi-permanent stent(e.g., intravenous, intraperitoneal, intracisternal or intracapsular)may be advisable. In Example below, intraspinal administration of AMIGO,AMIGO2 or AMIGO3 confer clearly detectable levels of restoration of lostor impaired central nervous system function.

Uses of AMIGO Compounds

The present invention employs AMIGO compounds for use in inhibiting thefunction of EGFR, ultimately modulating the phosphorylation of EGFR andthus modulating the signalling cascade initiated by EGFR. This isaccomplished by providing AMIGO compounds which specifically bind andmodulate EGFR phosphorylation. Such AMIGO compounds interfere with thenormal role of EGFR function and causes a modulation of its cellularsignaling. The functions of EGFR phosphorylation to be interferedinclude all vital functions such as, for example, ligand-receptorinteraction, dimerization of EGFR in the cell membrane, phosphorylationof EGFR, modulation of EGFR initiated signalling cascades which may beengaged in by EGFR. The overall effect of such interference with AMIGOcompounds is modulation of the phosphorylation of EGFR. In the contextof this invention, “modulation” means either an increase (stimulation)or a decrease (inhibition) in the phosphorylation of an EGFR. In thecontext of the present invention, inhibition is the preferred form ofmodulation of EGFR phosphorylation.

Some of the featured AMIGO compounds can be used to treat cellproliferative disorders characterized by inappropriate EGFR activity.“Inappropriate EGFR” activity refers to either: 1) EGF-receptor (EGFR)expression in cells which normally do not express EGFR; 2) EGFexpression by cells which normally do not express EGF/TGF-.alpha.; 3)increased EGF-receptor (EGFR) expression leading to unwanted cellproliferation; 4) increased EGF/TGF-.alpha. expression leading tounwanted cell proliferation; and/or 5) mutations leading to constitutiveactivation of EGF-receptor (EGFR). The existence of inappropriate orabnormal EGF/TGF-.alpha. and EGFR levels or activities is determined byprocedures well known in the art.

An increase in EGF/TGF-.alpha. activity or expression is characterizedby an increase in one or more of the activities which can occur upon EGFligand binding such as: (I) EGF-R dimerization; (2) auto-phosphorylationof EGFR, (3) phosphorylation of an EGFR substrate (e.g., PLC.gamma.),(4) activation of an adapter molecule, and/or (5) increased celldivision. These activities can be measured using techniques describedbelow and known in the art. For example auto-phosphorylation of EGFR canbe measured using an anti-phosphotyrosine antibody, and increased celldivision can be performed by measuring .sup.3H-thymidine incorporationinto DNA. Preferably, the increase in EGFR activity is characterized byan increased amount of phosphorylated EGFR and/or DNA synthesis.

Unwanted cell proliferation can result from inappropriate EGFR activityoccurring in different types of cells including cancer cells, cellssurrounding a cancer cell, and endothelial cells. Examples of disorderscharacterized by inappropriate EGF activity include cancers such asglioma, head, neck, gastric, lung, breast, ovarian, colon, and prostate.

AMIGO compound. The term “AMIGO compound” is meant to refer to an AMIGOpeptide, variants, biologically active fragments, antigenic fragment,anti-AMIGO antibodies or binding portion thereof and nucleic acidsencoding said peptides which are capable of binding to or interacting insome way with EGFR or a ligand of the epidermal growth factor receptor.Binding or interaction of an AMIGO compound of the invention with thecorresponding ligand results in the modulation, preferably prevention orinhibition, of the interaction between a ligand and its correspondingreceptor. Because the ligand-receptor interaction is involved in theproliferation of EGFR-expressing tumour cells, the term “an AMIGOcompound” is meant to include all compounds which modulate theinteraction between the epidermal growth factor receptor and theircorresponding ligands, more preferably adversely affect interactionbetween the epidermal growth factor receptor and their correspondingligands leading to inhibition of phosphorylation of EGFR.

As used herein, the terms “inhibits phosphorylation” (e.g., referring toinhibition/blocking of phosphorylation of EGFR) encompass both partialand complete inhibition. The inhibition of EGFR phosphorylationpreferably reduces or alters the normal level or type of cell signalingthat occurs when EGFR ligand binds to EGFR without inhibition orblocking. Inhibition is also intended to include any measurable decreasein the binding affinity of EGFR ligand to EGFR when in contact with anAMIGO compound as compared to the ligand not in contact with an AMIGOcompound, e.g., the blocking of EGFR ligands to EGFR by at least about10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 99%, or 100%.

The AMIGO compounds of the present invention have a multitude oftherapeutic and diagnostic uses. For example, therapeutic uses involvecancer therapy in a patient suspected of suffering from cancer or otherrelated diseases. Specifically, AMIGO compounds of the present inventioncan be used to treat patients that have tumour cells which produce theEGFR ligand and/or overexpress the EGFR proteins.

One type of treatment may involve the use of the AMIGO compounds coupledto a therapeutic agent. By administering an effective amount of AMIGOcompounds coupled with the therapeutic agent to a patient, a tumourcells in the patient which express EGFR can be growth inhibited orkilled, thereby providing a treatment for cancer.

In accordance with the method of cancer treatment of the invention, theconjugated AMIGO compound is capable of recognizing and binding totumour cells due to the association of the tumour cells with the EGFR.Without being limited, the mechanism of binding to the cancer cell mayinvolve the recognition of EGFR, ligand located on the cell surface orbecause of expression and/or secretion of the ligand.

Once the conjugated AMIGO compound is bound or in close association withthe tumour cell by interacting with EGFR, the therapeutic agent iscapable of inhibiting or killing that cell. In this manner, the therapyof the present invention is selective for a particular target, e.g.,cancer cells which are associated with the EGFR.

Normal cells and other cells not associated with the EGFR (cells whichdo not express EGFR) may not, for the most part, be affected by therapywith AMIGO compounds.

Alternatively, the AMIGO compounds of the present invention may be usedto prevent or inhibit inducement of tumour cell proliferation. Forexample, cancer cells which contain the EGFR are induced to proliferatein the presence of low concentrations of EGFR ligand. Preventing theEGFR ligand from interacting with its receptor may provide a means totreat a cancer patient.

According to the method of inhibiting or preventing cellularproliferation of the present invention, the AMIGO compound is capable ofbinding to the EGFR. Binding the EGFR in vivo forms an EGFR-AMIGOcompound complex and thus may prevent or inhibit the ligand-receptorinteraction either sterically or otherwise. Thus, the present inventionprovides a treatment to prevent or inhibit tumour cell proliferation ina patient by administering an effective amount of an AMIGO compound tosuch a patient.

It will be appreciated that a number of other therapeutic uses of theAMIGO compounds of the present invention may be devised. Such therapiesmay involve use of other known treatment techniques in combination withthe AMIGO compounds of the invention. The present invention is not meantto be limited to the therapeutic treatment described and are thus onlypresented by way of illustration.

Furthermore, administration of an amount of the AMIGO compounds of thepresent invention sufficient to inhibit or kill a tumour cell may varydepending upon a number of factors including the type of malignant cell,body weight of the patient, the type of therapeutic agent used and thelike. Those of skill in the art will appreciate that the amountnecessary to inhibit or kill a particular malignant cell in vitro or invivo can easily be determined with minimal routine experimentation. Aneffective amount of such AMIGO compounds may be administeredparenterally, subcutaneously, intravenously, intramuscularly,intraperitoneally or orally. In addition, pharmaceutical preparationsmay be prepared which contain suitable excipients, auxiliaries, orcompounds which facilitate processing or stability of the AMIGOcompounds of the invention as pharmaceutical agents.

Diagnostic uses of the AMIGO compounds of the present invention (due toits modification of EGFR phosphorylation) may include, for example,detection of EGFR in a sample obtained from a patient. Such samples maybe body tissue, body fluids (such as blood, urine, tear drops, saliva,serum, and cerebrospinal fluid), feces, cellular extracts and the like.

Assaying for the EGFR phosphorylation of the invention in a sampleobtained from a patient may thus provide for a method for diagnosingcancer. That is, detection of EGFR in a sample obtained from a patientindicates the presence of EGFR expressing cells in a patient.Furthermore, since the AMIGO compound is specific for, EGFR, thephosphorylation assay may provide information concerning the biology ofa patient's tumor. For example, cancer patients with a tumour cells thatoverexpress the EGFR are known to have poorer overall survival thancancer patients that do not show EGFR overexpression. Detection of EGFRphosphorylation may thus serve as a prognostic test, allowing theclinician to select a more effective therapy for treating the patient.

The AMIGO compound compositions of the invention can be initially testedfor binding activity associated with therapeutic or diagnostic use invitro. For example, compositions of the invention can be tested usingthe ELISA and flow cytometric assays described in the Examples below.Moreover, the activity of these molecules in triggering at least oneeffector-mediated effector cell activity, including phosphorylation ofEGFR of cells expressing EGFR can be assayed.

The compositions of the invention have additional utility in therapy anddiagnosis of EGFR-related diseases. For example, the AMIGO DNA can beused to elicit in vivo or in vitro one or more of the followingbiological activities: to inhibit EGF or TGF-.alpha. inducedautophosphorylation in a cell expressing EGFR; to inhibit autocrine EGFor TGF-.alpha.-induced activation of a cell expressing EGFR; or toinhibit the growth of a cell expressing EGFR, e.g., at low dosages.

In a particular embodiment, the AMIGO compounds and derivatives/variantsthereof are used in vivo to treat, prevent or diagnose a variety ofEGFR-related diseases. Examples of EGFR-related diseases include avariety of cancers, such as glioma, glioblastoma, bladder, breast,uterine/cervical, colon, pancreatic, colorectal, kidney, stomach,ovarian, prostate, renal cell, squamous cell, lung (non-small cell),esophageal, and head and neck cancer.

Methods of administering the compositions of the invention are known inthe art. Suitable dosages of the molecules used will depend on the ageand weight of the subject and the particular drug used. The AMIGOcompounds can be coupled to radionuclides, such as 131I, 90Y, 105Rh,indium-111, etc., as described in Goldenberg, D. M. et al. (1981) CancerRes. 41: 4354-4360, and in EP 0365 997. In another aspect the inventionrelates to an immunoconjugate comprising an AMIGO antibody or bindingportion thereof or AMIGO peptide or fragment according to the inventionlinked to a radioisotope, cytotoxic agent (e.g., calicheamicin andduocarmycin), a cytostatic agent, or a chemotherapeutic drug. Thecompositions of the invention can also be coupled to anti-infectiousagents.

In another embodiment, the AMIGO compounds can be co-administered with atherapeutic agent, e.g., a chemotherapeutic agent, an immunosuppressiveagent, or can be co-administered with other known therapies, such asphysical therapies, e.g., radiation therapy, hyperthermia, ortransplantation (e.g., bone marrow transplantation). Such therapeuticagents include, among others, anti-neoplastic agents such as doxorubicin(adriamycin), cisplatin bleomycin sulfate, carmustine, chlorambucil, andcyclophosphamide hydroxyurea which, by themselves, are only effective atlevels which are toxic or subtoxic to a patient. Cisplatin isintravenously administered as a 100 mg/m.sup.2 dose once every fourweeks and adriamycin is intravenously administered as a 60-75 mg/m.sup.2dose once every 21 days.

Pharmaceutical compositions of the present invention can include one ormore further chemotherapeutic agents selected from the group consistingof nitrogen mustards (e.g., cyclophosphamide and ifosfamide), aziridines(e.g., thiotepa), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g.,carmustine and streptozocin), platinum complexes (e.g., carboplatin andcisplatin), non-classical alkylating agents (e.g., dacarbazine andtemozolamide), folate analogs (e.g., methotrexate), purine analogs(e.g., fludarabine and mercaptopurine), adenosine analogs (e.g.,cladribine and pentostatin), pyrimidine analogs (e.g., fluorouracil(alone or in combination with leucovorin) and gemcitabine), substitutedureas (e.g., hydroxyurea), antitumor antibiotics (e.g., bleomycin anddoxorubicin), epipodophyllotoxins (e.g., etoposide and teniposide),microtubule agents (e.g., docetaxel and paclitaxel), camptothecinanalogs (e.g., irinotecan and topotecan), enzymes (e.g., asparaginase),cytokines (e.g., interleukin-2 and interferon-.alpha.), monoclonalantibodies (e.g., trastuzumab and bevacizumab), recombinant toxins andimmunotoxins (e.g., recombinant cholera toxin-B and TP-38), cancer genetherapies, physical therapies (e.g., hyperthermia, radiation therapy,and surgery) and cancer vaccines (e.g., vaccine against telomerase).

Co-administration of the AMIGO compounds of the present invention withchemotherapeutic agents provides two anti-cancer agents which operatevia different mechanisms which yield a cytotoxic effect to human tumorcells. Such co-administration can solve problems due to development ofresistance to drugs or a change in the antigenicity of the tumor cellswhich would render them unreactive with the antibody.

In another embodiment, the subject can be additionally treated with alymphokine preparation. Cancer cells which do not highly express EGFRcan be induced to do so using lymphokine preparations. Lymphokinepreparations can cause a more homogeneous expression of EGFRs amongcells of a tumor which can lead to a more effective therapy.

Lymphokine preparations suitable for administration includeinterferon-gamma, tumor necrosis factor, and combinations thereof. Thesecan be administered intravenously. Suitable dosages of lymphokine are10,000 to 1,000,000 units/patient.

In one embodiment, the invention provides methods for detecting thepresence of EGFR phosphorylation in a sample, or measuring the amount ofEGFR phosphorylation, comprising contacting the sample, and a controlsample, with an AMIGO compound, which specifically binds to EGFR, underconditions that allow for formation of a complex between the AMIGOcompound and EGFR. The formation of a complex is then detected, i.e.modulation, preferably inhibition of phosphorylation, wherein adifference in EGFR phosphorylation between the sample compared to thecontrol sample is indicative the presence of EGFR in the sample.

Screening

The present invention also encompasses agent which modulate AMIGOexpression or activity. An agent may, for example, be a small molecule.For example, such small molecules include, but are not limited to,peptides, peptidomimetics (e.g., peptoids), amino acids, amino acidanalogs, polynucleotides, polynucleotide analogs, nucleotides,nucleotide analogs, organic or inorganic compounds (i.e,. includingheteroorganic and organometallic compounds) having a molecular weightless than about 10,000 grams per mole, organic or inorganic compoundshaving a molecular weight less than about 5,000 grams per mole, organicor inorganic compounds having a molecular weight less than about 1,000grams per mole, organic or inorganic compounds having a molecular weightless than about 500 grams per mole, and salts, esters, and otherpharmaceutically acceptable forms of such compounds. It is understoodthat appropriate doses of small molecule agents depends upon a number offactors within the ken of the ordinarily skilled physician,veterinarian, or researcher. The dose(s) of the small molecule willvary, for example, depending upon the identity, size, and condition ofthe subject or sample being treated, further depending upon the route bywhich the composition is to be administered, if applicable, and theeffect which the practitioner desires the small molecule to have uponthe nucleic acid or polypeptide of the invention. Exemplary dosesinclude milligram or microgram amounts of the small molecule perkilogram of subject or sample weight (e.g., about 1 microgram perkilogram to about 500 milligrams per kilogram, about 100 micrograms perkilogram to about 5 milligrams per kilogram, or about 1 microgram perkilogram to about 50 micrograms per kilogram. It is furthermoreunderstood that appropriate doses of a small molecule depend upon thepotency of the small molecule with respect to the expression or activityto be modulated. Such appropriate doses may be determined using theassays described herein. When one or more of these small molecules is tobe administered to an animal (e.g., a human) in order to modulateexpression or activity of a polypeptide or nucleic acid of theinvention, a physician, veterinarian, or researcher may, for example,prescribe a relatively low dose at first, subsequently increasing thedose until an appropriate response is obtained. In addition, it isunderstood that the specific dose level for any particular animalsubject will depend upon a variety of factors including the activity ofthe specific compound employed, the age, body weight, general health,gender, and diet of the subject, the time of administration, the routeof administration, the rate of excretion, any drug combination, and thedegree of expression or activity to be modulated.

The subject methods include screens for agents which modulate homophilicor heterophilic AMIGO interactions and methods for modulating theseinteractions. AMIGO activation is found to regulate a wide variety ofcell functions, including cell-cell interactions, cell mobility, neuritegrowth and fasciculation. AMIGO polypeptides are disclosed as specificmodulators of function of EGFR polypeptides. Accordingly, the inventionprovides methods for modulating targeted cell function comprising thestep of modulating AMIGO activation by contacting the cell with amodulator of a AMIGO:AMIGO or AMIGO:AMIGO ligand interaction. Theinvention also provides methods for modulating targeted cell functioncomprising the step of modulating EGFR activation by contacting the cellwith a modulator of a AMIGO:EGFR interaction.

In another aspect, the invention provides methods of screening foragents which modulate AMIGO:AMIGO, AMIGO:EGFR or AMIGO:AMIGO ligandinteractions. These methods generally involve forming a mixture of anAMIGO-expressing cell, an AMIGO, EGFR or AMIGO ligand polypeptide and acandidate agent, and determining the effect of the agent on the amountof AMIGO expressed by the cell. The methods are amenable to automated,cost-effective high throughput screening of chemical libraries for leadcompounds. Identified reagents find use in the pharmaceutical industriesfor animal and human trials; for example, the reagents may bederivatized and rescreened in vitro and in vivo assays to optimizeactivity and minimize toxicity for pharmaceutical development. Morespecifically, neuronal cell based neural outgrowth assays, fasciculationand aggregation assays are described in detail in the experimentalsection below.

The invention further provides methods (also referred to herein as“screening assays”) for identifying modulators, i.e., candidate or testcompounds or agents (e.g., peptides, peptidomimetics, peptoids, smallmolecules or other drugs) which bind to AMIGO proteins, have astimulatory or inhibitory effect on, for example, AMIGO expression orAMIGO activity, or have a stimulatory or inhibitory effect on, forexample, the expression or activity of an AMIGO substrate. Compoundsthus identified can be used to modulate the activity of AMIGOs in atherapeutic protocol, to elaborate the biological function of the AMIGO,or to identify compounds that disrupt normal AMIGO interactions. Thepreferred AMIGOs used in this embodiment are the AMIGO, AMIGO2 andAMIGO3 of the present invention.

In one embodiment, the invention provides assays for screening candidateor test compounds which are substrates of an AMIGO protein orpolypeptide or biologically active portion thereof. In anotherembodiment, the invention provides assays for screening candidate ortest compounds which bind to or modulate the activity of an AMIGOprotein or polypeptide or biologically active portion thereof.

The test compounds of the present invention can be obtained using any ofthe numerous approaches in combinatorial library methods known in theart, including: biological libraries; peptoid libraries [libraries ofmolecules having the functionalities of peptides, but with a novel,non-peptide backbone which are resistant to enzymatic degradation butwhich nevertheless remain bioactive] (see, e.g., Zuckermann, R. N. etal. J. Med. Chem. 1994, 37: 2678-85); spatially addressable parallelsolid phase or solution phase libraries; synthetic library methodsrequiring deconvolution; the ‘one-bead one-compound’ library method; andsynthetic library methods using affinity chromatography selection. Thebiological library and peptoid library approaches are limited to peptidelibraries, while the other four approaches are applicable to peptide,non-peptide oligomer or small molecule libraries of compounds (Lam, K.S. (1997) Anticancer Drug Des. 12:145).

In one embodiment, an assay is a cell-based assay in which a cell whichexpresses an AMIGO protein or biologically active portion thereof iscontacted with a test compound and the ability of the test compound tomodulate AMIGO activity is determined. Determining the ability of thetest compound to modulate AMIGO activity can be accomplished bymonitoring, for example, cell attachment or adhesion, cell growth,neurite outgrowth, fasciculation and cell chemotaxis. The cell, forexample, can be of mammalian origin, e.g., a neuronal cell. In preferredembodiment, AMIGO is expressed in neuronal cells and the ability of thetest compound to modulate AMIGO activity is accomplished by monitoringneurite outgrowth or alternatively, by monitoring axonal fasciculation.In another prererred embodiment AMIGO and EGFR are co-expressed, e.g. intumour cells of neuronal or non-neuronal origin, and the amount ofphosphorylation of EGFR in monitored.

Determining the ability of the AMIGO protein or a biologically activefragment thereof, to bind to or interact with an AMIGO target molecule(comprising for example AMIGO, EGFR or AMIGO ligand) can be accomplishedby one of the methods described above for determining direct binding. Ina preferred embodiment, determining the ability of the AMIGO protein tobind to or interact with an AMIGO target molecule can be accomplished bydetermining the activity of the target molecule. For example, theactivity of the target molecule can be determined by detecting inductionof a cellular second messenger of the target (i.e., intracellularcalcium or IP3), detecting catalytic/enzymatic activity of the targetmolecule upon an appropriate substrate, detecting the induction of areporter gene (comprising a target-responsive regulatory elementoperatively linked to a nucleic acid encoding a detectable marker, e.g.,luciferase), or detecting a target-regulated cellular response (i.e.,cell attachment, adhesion, growth or migration).

In yet another embodiment, an assay of the present invention is acell-free assay in which an AMIGO protein or biologically active portionthereof is contacted with a test compound and the ability of the testcompound to bind to the AMIGO protein or biologically active portionthereof is determined. Preferred biologically active portions of theAMIGO proteins to be used in assays of the present invention includefragments which participate in interactions with AMIGO, EGFR or AMIGOligand protein. Preferably, these fragments comprise extracellular partsof the AMIGO or EGFR proteins.

The cell-free assays of the present invention are amenable to use ofboth soluble and/or membrane-bound forms of isolated AMIGO proteins orbiologically active portions thereof. In the case of cell-free assays inwhich a membrane-bound form of an AMIGO protein is used it may bedesirable to utilize a solubilizing agent such that the membrane-boundform of the isolated protein is maintained in solution. Examples of suchsolubilizing agents include non-ionic detergents such asn-octylglucoside, n-dodecylglucoside, n-dodecylmaltoside,octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, Triton™ X-100,Triton™ X-14, Thesit™, Isotridecypoly(ethylene glycol ether)n,3-[(3-cholamidopropyl)dimethylamminio]-1-propane sulfonate (CHAPS),3-[(3-cholamidopropyl)dimethylamminio]-2-hydroxy-1-propane sulfonate(CHAPSO), or N-dodecyl=N,N-dimethyl-3-ammonio-1-propane sulfonate.

The principle of the assays used to identify compounds that bind to theAMIGO protein involves preparing a reaction mixture of the AMIGO proteinand the test compound under conditions and for a time sufficient toallow the two components to interact and bind, thus forming a complexthat can be removed and/or detected in the reaction mixture. Theseassays can be conducted in a variety of ways. For example, one method toconduct such an assay would involve anchoring AMIGO protein or the testsubstance onto a solid phase and detecting AMIGO protein/test compoundcomplexes anchored on the solid phase at the end of the reaction. In oneembodiment of such a method, AMIGO protein can be anchored onto a solidsurface, and the test compound, (which is not anchored), can be labeled,either directly or indirectly, with detectable labels discussed hereinand which are well-known to one skilled in the art.

In more than one embodiment of the above assay methods of the presentinvention, it may be desirable to immobilize either AMIGO, EGFR or AMIGOligand to facilitate separation of complexed from uncomplexed forms ofone or both of the proteins, as well as to accommodate automation of theassay. Binding of a test compound to an AMIGO protein, or interaction ofan AMIGO protein with AMIGO, EGFR or AMIGO ligand in the presence andabsence of a candidate compound, can be accomplished in any vesselsuitable for containing the reactants. Examples of such vessels includemicrotiter plates, test tubes, and micro-centrifuge tubes. In oneembodiment, a fusion protein can be provided which adds a domain thatallows one or both of the proteins to be bound to a matrix. For example,glutathione-S-transferase/AMIGO fusion proteins orglutathione-S-transfera-se/target fusion proteins can be adsorbed ontoglutathione sepharose beads (Sigma Chemical, St. Louis, Mo.) orglutathione derivatized microtiter plates, which are then combined withthe test compound or the test compound and either the non-adsorbedAMIGO, EGFR or AMIGO ligand protein, and the mixture incubated underconditions conducive to complex formation (e.g., at physiologicalconditions for salt and pH). Following incubation, the beads ormicrotiter plate wells are washed to remove any unbound components, thematrix immobilized in the case of beads, complex determined eitherdirectly or indirectly, for example, as described above. Alternatively,the complexes can be dissociated from the matrix, and the level of AMIGObinding or activity determined using standard techniques.

In order to conduct the assay, the nonimmobilized component is added tothe coated surface containing the anchored component. After the reactionis complete, unreacted components are removed (e.g., by washing) underconditions such that any complexes formed will remain immobilized on thesolid surface. The detection of complexes anchored on the solid surfacecan be accomplished in a number of ways. Where the previouslynonimmobilized component is pre-labeled, the detection of labelimmobilized on the surface indicates that complexes were formed. Wherethe previously nonimmobilized component is not pre-labeled, an indirectlabel can be used to detect complexes anchored on the surface; e.g.,using a labeled antibody specific for the immobilized component (theantibody, in turn, can be directly labeled or indirectly labeled with,e.g., a labeled anti-Ig antibody).

In one embodiment, this assay is performed utilizing antibodies reactivewith AMIGO protein, EGFR or AMIGO ligand but which do not interfere withbinding of the AMIGO protein to AMIGO, EGFR or AMIGO ligand. Suchantibodies can be derivatized to the wells of the plate, and AMIGO,EGFR, or AMIGO ligand trapped in the wells by antibody conjugation.Methods for detecting such complexes, in addition to those describedabove for the GST-immobilized complexes, include immunodetection ofcomplexes using antibodies reactive with the AMIGO, EGFR or AMIGOligand, as well as enzyme-linked assays which rely on detecting anenzymatic activity associated with the AMIGO protein, EGFR or AMIGOligand.

Alternatively, in another embodiment, an assay can be conducted in aliquid phase. In such an assay, the reaction products are separated fromunreacted components, by any of a number of standard techniques,including but not limited to: differential centrifugation,chromatography, electrophoresis and immunoprecipitation. In differentialcentrifugation, complexes of molecules may be separated from uncomplexedmolecules through a series of centrifugal steps, due to the differentsedimentation equilibria of complexes based on their different sizes anddensities (see, for example, Rivas, G., and Minton, A. P., TrendsBiochem Sci 1993 August;18(8):284-7). Standard chromatographictechniques may also be utilized to separate complexed molecules fromuncomplexed ones. For example, gel filtration chromatography separatesmolecules based on size, and through the utilization of an appropriategel filtration resin in a column format, for example, the relativelylarger complex may be separated from the relatively smaller uncomplexedcomponents. Similarly, the relatively different charge properties of thecomplex as compared to the uncomplexed molecules may be exploited todifferentially separate the complex from the remaining individualreactants, for example through the use of ion-exchange chromatographyresins. Such resins and chromatographic techniques are well known to oneskilled in the art (see, e.g., Heegaard, N. H., J Mol Recognit 1998Winter; 11(1-6):141-8; Hage, D. S., and Tweed, S. A. J Chromatogr BBiomed Sci Appl 1997 Oct. 10;699(1-2):499-525). Gel electrophoresis mayalso be employed to separate complexed molecules from unbound species(see, e.g., Ausubel, F. et al., eds. Current Protocols in MolecularBiology 1999, J. Wiley: New York.). In this technique, protein ornucleic acid complexes are separated based on size or charge, forexample. In order to maintain the binding interaction during theelectrophoretic process, nondenaturing gels in the absence of reducingagent are typically preferred, but conditions appropriate to theparticular interactants will be well known to one skilled in the art.Immunoprecipitation is another common technique utilized for theisolation of a protein-protein complex from solution (see, for example,Ausubel, F. et al., eds. Current Protocols in Molecular Biology 1999, J.Wiley: New York). In this technique, all proteins binding to an antibodyspecific to one of the binding molecules are precipitated from solutionby conjugating the antibody to a polymer bead that may be readilycollected by centrifugation. The bound proteins are released from thebeads (through a specific proteolysis event or other technique wellknown in the art which will not disturb the protein-protein interactionin the complex), and a second immunoprecipitation step is performed,this time utilizing antibodies specific for a different interactingprotein. In this manner, only the complex should remain attached to thebeads. The captured complex may be visualized using gel electrophoresis.The presence of a molecular complex (which may be identified by any ofthese techniques) indicates that a specific binding event has occurred,and that the introduced compound specifically binds to the targetprotein. Further, fluorescence energy transfer may also be convenientlyutilized, as described herein, to detect binding without furtherpurification of the complex from solution.

In a preferred embodiment, the assay includes contacting the AMIGOprotein or biologically active portion thereof with a known compoundwhich binds AMIGO to form an assay mixture, contacting the assay mixturewith a test compound, and determining the ability of the test compoundto interact with an AMIGO protein, wherein determining the ability ofthe test compound to interact with an AMIGO protein comprisesdetermining the ability of the test compound to preferentially bind toAMIGO or biologically active portion thereof as compared to the knowncompound. In further preferred embodiment, AMIGO protein or biologicallyactive portion thereof is contacted with AMIGO protein and the abilityof the test compound to interact with AMIGO is compared to knownAMIGO:AMIGO interaction. In a still further embodiment, AMIGO protein orbiologically active portion thereof is contacted with EGFR protein andthe ability of the test compound to interact with AMIGO is compared toknown AMIGO:EGFR interaction.

In yet another embodiment, the cell-free assay involves contacting anAMIGO protein or biologically active portion thereof with a knowncompound which binds the AMIGO protein to form an assay mixture,contacting the assay mixture with a test compound, and determining theability of the test compound to interact with the AMIGO protein, whereindetermining the ability of the test compound to interact with the AMIGOprotein comprises determining the ability of the AMIGO protein topreferentially bind to or modulate the activity of an AMIGO, EGFR orAMIGO ligand.

The AMIGO proteins of the invention can, in vivo, interact with one ormore cellular or extracellular macromolecules, such as proteins. For thepurposes of this discussion, such cellular and extracellularmacromolecules are referred to herein as “binding partners.” Compoundsthat disrupt such interactions can be useful in regulating the activityof the AMIGOs. Such compounds can include, but are not limited tomolecules such as antibodies, peptides, and small molecules. Thepreferred proteins for use in this embodiment are the AMIGO proteinsherein identified. Towards this purpose, in an alternative embodiment,the invention provides methods for determining the ability of the testcompound to modulate the activity of an AMIGO protein through modulationof the activity of a downstream effector of an AMIGO, EGFR or AMIGOligand. For example, the activity of the effector molecule on an AMIGO,EGFR or AMIGO ligand can be determined, or the binding of the effectorto AMIGO, EGFR or AMIGO ligand can be determined as previouslydescribed.

The basic principle of the assay systems used to identify compounds thatinterfere with the interaction between the AMIGO and its cellular orextracellular binding partner or partners involves preparing a reactionmixture containing the AMIGO, and the binding partner under conditionsand for a time sufficient to allow the two products to interact andbind, thus forming a complex. In order to test an agent for inhibitoryactivity, the reaction mixture is prepared in the presence and absenceof the test compound. The test compound can be initially included in thereaction mixture, or can be added at a time subsequent to the additionof the AMIGO and its cellular or extracellular binding partner. Controlreaction mixtures are incubated without the test compound or with aplacebo. The formation of any complexes between the AMIGO and thecellular or extracellular binding partner is then detected. Theformation of a complex in the control reaction, but not in the reactionmixture containing the test compound, indicates that the compoundinterferes with the interaction of the AMIGO and the interactive bindingpartner. Additionally, complex formation within reaction mixturescontaining the test compound and AMIGO can also be compared to complexformation within reaction mixtures containing the test compound andmutant AMIGO. This comparison can be important in those cases wherein itis desirable to identify compounds that disrupt interactions of mutantbut not normal AMIGOs.

The assay for compounds that interfere with the interaction of theAMIGOs and binding partners can be conducted in a heterogeneous orhomogeneous format. Heterogeneous assays involve anchoring either theAMIGO or the binding partner onto a solid phase and detecting complexesanchored on the solid phase at the end of the reaction. In homogeneousassays, the entire reaction is carried out in a liquid phase. In eitherapproach, the order of addition of reactants can be varied to obtaindifferent information about the compounds being tested. For example,test compounds that interfere with the interaction between the AMIGOsand the binding partners, e.g., by competition, can be identified byconducting the reaction in the presence of the test substance; i.e., byadding the test substance to the reaction mixture prior to orsimultaneously with the AMIGO and interactive cellular or extracellularbinding partner. Alternatively, test compounds that disrupt preformedcomplexes, e.g., compounds with higher binding constants that displaceone of the components from the complex, can be tested by adding the testcompound to the reaction mixture after complexes have been formed. Thevarious formats are briefly described below.

In a heterogeneous assay system, either the AMIGO or the interactivecellular or extracellular binding partner, is anchored onto a solidsurface, while the non-anchored species is labeled, either directly orindirectly. In practice, microtitre plates are conveniently utilized.The anchored species can be immobilized by non-covalent or covalentattachments. Non-covalent attachment can be accomplished simply bycoating the solid surface with a solution of the AMIGO or bindingpartner and drying. Alternatively, an immobilized antibody specific forthe species to be anchored can be used to anchor the species to thesolid surface. The surfaces can be prepared in advance and stored.

In order to conduct the assay, the partner of the immobilized species isexposed to the coated surface with or without the test compound. Afterthe reaction is complete, unreacted components are removed (e.g., bywashing) and any complexes formed will remain immobilized on the solidsurface. The detection of complexes anchored on the solid surface can beaccomplished in a number of ways. Where the non-immobilized species ispre-labeled, the detection of label immobilized on the surface indicatesthat complexes were formed. Where the non-immobilized species is notpre-labeled, an indirect label can be used to detect complexes anchoredon the surface; e.g., using a labeled antibody specific for theinitially non-immobilized species (the antibody, in turn, can bedirectly labeled or indirectly labeled with, e.g., a labeled anti-Igantibody). Depending upon the order of addition of reaction components,test compounds that inhibit complex formation or that disrupt preformedcomplexes can be detected.

Alternatively, the reaction can be conducted in a liquid phase in thepresence or absence of the test compound, the reaction productsseparated from unreacted components, and complexes detected; e.g., usingan immobilized antibody specific for one of the binding components toanchor any complexes formed in solution, and a labeled antibody specificfor the other partner to detect anchored complexes. Again, dependingupon the order of addition of reactants to the liquid phase, testcompounds that inhibit complex or that disrupt preformed complexes canbe identified.

In an alternate embodiment of the invention, a homogeneous assay can beused. In this approach, a preformed complex of the AMIGO and theinteractive cellular or extracellular binding partner product isprepared in that either the AMIGOs or their binding partners arelabeled, but the signal generated by the label is quenched due tocomplex formation (see, e.g., U.S. Pat. No. 4,109,496 that utilizes thisapproach for immunoassays). The addition of a test substance thatcompetes with and displaces one of the species from the preformedcomplex will result in the generation of a signal above background. Inthis way, test substances that disrupt AMIGO-cellular or extracellularbinding partner interaction can be identified.

Assays for the Detection of the Ability of a Test Compound to ModulateExpression of AMIGO

In another embodiment, modulators of AMIGO expression are identified ina method wherein a cell is contacted with a candidate compound and theexpression of AMIGO mRNA or protein in the cell is determined. The levelof expression of AMIGO mRNA or protein in the presence of the candidatecompound is compared to the level of expression of AMIGO mRNA or proteinin the absence of the candidate compound. The candidate compound canthen be identified as a modulator of AMIGO expression based on thiscomparison. For example, when expression of AMIGO mRNA or protein isgreater (statistically significantly greater) in the presence of thecandidate compound than in its absence, the candidate compound isidentified as a stimulator of AMIGO mRNA or protein expression.Alternatively, when expression of AMIGO mRNA or protein is less(statistically significantly less) in the presence of the candidatecompound than in its absence, the candidate compound is identified as aninhibitor of AMIGO mRNA or protein expression. The level of AMIGO mRNAor protein expression in the cells can be determined by methodsdescribed herein for detecting AMIGO mRNA or protein.

Combination Assays

In another aspect, the invention pertains to a combination of two ormore of the assays described herein. For example, a modulating agent canbe identified using a cell-based or a cell free assay, and the abilityof the agent to modulate the activity of an AMIGO protein can beconfirmed in vivo, e.g., in an animal such as an animal model for CNSdisorders, or for cellular transformation and/or neuronal regeneration.

This invention farther pertains to novel agents identified by theabove-described screening assays. Accordingly, it is within the scope ofthis invention to further use an agent identified as described herein inan appropriate animal model. For example, an agent identified asdescribed herein (e.g., an AMIGO modulating agent, an antisense AMIGOnucleic acid molecule, an AMIGO-specific antibody, or an AMIGO-bindingpartner) can be used in an animal model to determine the efficacy,toxicity, or side effects of treatment with such an agent.Alternatively, an agent identified as described herein can be used in ananimal model to determine the mechanism of action of such an agent.Furthermore, this invention pertains to uses of novel agents identifiedby the above-described screening assays for treatments as describedherein.

The choice of assay format will be based primarily on the nature andtype of sensitivity/resistance protein being assayed. A skilled artisancan readily adapt protein activity assays for use in the presentinvention with the genes identified herein.

Diagnostics

The invention also features diagnostic or prognostic kits for use indetecting the presence of AMIGO or allelic variant thereof in abiological sample. The kit provides means for the diagnostics of AMIGOdependent conditions as described hereinabove or for assessing thepredisposition of an individual to conditions mediated by variation ordysfunction of AMIGO. The kit can comprise a labeled compound capable ofdetecting AMIGO polypeptide or nucleic acid (e.g. mRNA) in a biologicalsample. The kit can also comprise nucleic acid primers or probes capableof hybridising specifically to at least of portion of an AMIGO gene orallelic variant thereof. The kit can be packaged in a suitable containerand preferably it contains instructions for using the kit.

Purification of AMIGO Binding Molecules

In yet another aspect of the invention, the AMIGO or AMIGO analog may beused for affinity purification of molecules (receptors) that bind to theAMIGO. AMIGO is a preferred ligand for purification. Briefly, thistechnique involves: (a) contacting a source of AMIGO receptor with animmobilized AMIGO under conditions whereby the AMIGO receptor to bepurified is selectively adsorbed onto the immobilized AMIGO; (b) washingthe immobilized AMIGO and its support to remove non-adsorbed material;and (c) eluting the AMIGO receptor molecules from the immobilized AMIGOto which they are adsorbed with an elution buffer. In a particularlypreferred embodiment of affinity purification, AMIGO is covalentlyattaching to an inert and porous matrix or resin (e.g., agarose reactedwith cyanogen bromide). Especially preferred is an AMIGO immunoadhesinimmobilized on a protein-A column. A solution containing AMIGO receptoris then passed through the chromatographic material. The AMIGO receptoradsorbs to the column and is subsequently released by changing theelution conditions (e.g. by changing pH or ionic strength).

The preferred technique for identifying molecules which bind to theAMIGO utilizes a chimeric AMIGO (e.g., epitope-tagged AMIGO or AMIGOimmunoadhesin) attached to a solid phase, such as the well of an assayplate. The binding of the candidate molecules, which are optionallylabelled (e.g., radiolabeled), to the immobilized AMIGO can be measured.

Production of Transgenic Animals

Nucleic acids which encode AMIGO, preferably from non-human species,such as murine or rat protein, can be used to generate either transgenicanimals or “knock out” animals which, in turn, are useful in thedevelopment and screening of therapeutically useful reagents. Atransgenic animal (e.g., a mouse) is an animal having cells that containa transgene, which transgene was introduced into the animal or anancestor of the animal at a prenatal, e.g., an embryonic, stage. Atransgene is a DNA which is integrated into the genome of a cell fromwhich a transgenic animal develops. In one embodiment, the human and/ormouse cDNA encoding AMIGO, or an appropriate sequence thereof, can beused to clone genomic DNA encoding AMIGO in accordance with establishedtechniques and the genomic sequences used to generate transgenic animalsthat contain cells which express DNA encoding AMIGO. Methods forgenerating transgenic animals, particularly animals such as mice, havebecome conventional in the art and are described, for example, in U.S.Pat. Nos. 4,736,866 and 4,870,009. Typically, particular cells would betargeted for AMIGO transgene incorporation with tissue-specificenhancers, which could result in desired effect of treatment. Transgenicanimals that include a copy of a transgene encoding AMIGO introducedinto the germ line of the animal at an embryonic stage can be used toexamine the effect of increased expression of DNA encoding AMIGO. Suchanimals can be used as tester animals for reagents thought to conferprotection from, for example, diseases related to AMIGO. In accordancewith this facet of the invention, an animal is treated with the reagentand a reduced incidence of the disease, compared to untreated animalsbearing the transgene, would indicate a potential therapeuticintervention for the disease.

It is now well-established that transgenes are expressed moreefficiently if they contain introns at the 5′ end, and if these are thenaturally occurring introns (Brinster et al. Proc. Natl. Acad. Sci. USA85:836-840 (1988); Yokode et al., Science 250:1273-1275 (1990)).

Transgenic offspring are identified by demonstrating incorporation ofthe microinjected transgene into their genomes, preferably by preparingDNA from short sections of tail and analyzing by Southern blotting forpresence of the transgene (“Tail Blots”). A preferred probe is a segmentof a transgene fusion construct that is uniquely present in thetransgene and not in the mouse genome. Alternatively, substitution of anatural sequence of codons in the transgene with a different sequencethat still encodes the same peptide yields a unique region identifiablein DNA and RNA analysis. Transgenic “founder” mice identified in thisfashion are bred with normal mice to yield heterozygotes, which arebackcrossed to create a line of transgenic mice. Tail blots of eachmouse from each generation are examined until the strain is establishedand homozygous. Each successfully created founder mouse and its strainvary from other strains in the location and copy number of transgenesinserted into the mouse genome, and hence have widely varying levels oftransgene expression. Selected animals from each established line aresacrificed at 2 months of age and the expression of the transgene isanalyzed by Northern blotting of RNA from liver, muscle, fat, kidney,brain, lung, heart, spleen, gonad, adrenal and intestine.

Production of “Knock Out” Animals

Alternatively, the non-human homologs of AMIGO can be used to constructan AMIGO “knock out” animal, i.e., having a defective or altered geneencoding AMIGO, as a result of homologous recombination between theendogenous AMIGO gene and an altered genomic AMIGO DNA introduced intoan embryonic cell of the animal. For example, murine AMIGO cDNA can beused to clone genomic AMIGO DNA in accordance with establishedtechniques. A portion of the genomic AMIGO DNA can be deleted orreplaced with another gene, such as a gene encoding a selectable markerwhich can be used to monitor integration. Typically, several kilobasesof unaltered flanking DNA (both at the 5′ and 3′ ends) are included inthe vector (see e.g., Thomas and Capecchi, Cell 51:503 (1987) for adescription of homologous recombination vectors). The vector isintroduced into an embryonic stem cell line (e.g., by electroporation)and cells in which the introduced DNA has homologously recombined withthe endogenous DNA are selected (see e.g., Li et al., Cell 69:915(1992)). The selected cells are then injected into a blastocyst of ananimal (e.g., a mouse) to form aggregation chimeras (see e.g., Bradley,in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E.J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152). A chimeric embryocan then be implanted into a suitable pseudopregnant female fosteranimal and the embryo brought to term to create a “knock out” animal.Progeny harbouring the homologously recombined DNA in their germ cellscan be identified by standard techniques and used to breed animals inwhich all cells of the animal contain the homologously recombined DNA.Knockout animals can be characterized for their ability to mimic humanneurological disorders and defects.

Equivalents

Although particular embodiments have been disclosed herein in detail,this has been done by way of example for purposes of illustration only,and is not intended to be limiting with respect to the scope of theappended claims that follow. In particular, it is contemplated by theinventors that various substitutions, alterations, and modifications maybe made to the invention without departing from the spirit and scope ofthe invention as defined by the claims. The choice of nucleic acidstarting material, clone of interest, or library type is believed to bea matter of routine for a person of ordinary skill in the art withknowledge of the embodiments described herein. Other aspects,advantages, and modifications considered to be within the scope of thefollowing claims.

Experimental Section

Materials and Methods

Ordered Differential Display

Ordered Differential Display was performed as described by Matz et al.(1997) comparing genes induced on amphoterin versus laminin matrix.Hippocampi were dissected from 18-d-old rat embryos and triturated withpasteur pipette in Hank's balanced salt solution (HBSS w/o Ca & Mg,GIBCO BRL) containing 1 mM sodium pyruvate and 10 mM Hepes, pH 7.4.After washing in HBSS, neurons were suspended in Neurobasal medium(GIBCO BRL), 2% B27 supplement (GIBCO BRL), 25 μM L-glutamic acid(Sigma-Aldrich), and 1% L-glutamine (GIBCO BRL) and they were thenseeded at the density of 10⁶ cells on 35 mm plastic plates (Greiner)coated with laminin (10 μg/ml; Sigma-Aldrich) or recombinant amphoterin(10 μg/ml). RNA was isolated by using RNeasy mini kit (Qiagen) 24 hoursafter seeding and was used for ordered differential display.

Cloning of the AMIGO, AMIGO2 and AMIGO3 cDNAs

The rat AMIGO cDNA 5′ end was amplificated by using method of Matz etal. (1999) based on template-switching effect and step-out PCR, and thefull-length cDNA was cloned from postnatal day 14 rat cerebrum usingRT-reaction with the following primers: 5′ primer ACTGCTTCTCGCCTGGCCCGT(SEQ ID NO: 42); and 3′ primer GAACCTCCCCATCAGCCTATACTG (SEQ ID NO: 43).The rat AMIGO sequence was used to find out human and mouse ESTs to getsequences for cloning of the human and mouse AMIGOs. The human AMIGOcDNA was cloned from the THP-1 cell-line (ATCC #TIB-202) using anRT-reaction with the following primers: 5′ primer CAGAACATGCCCGGGTGAC(SEQ ID NO: 44); and 3′ primer GGACCAATTCCCTTGAGGTCAG (SEQ ID NO: 45).The mouse AMIGO cDNA was cloned from adult mouse cerebrum using anRT-reaction with the following primers: 5′ primer ACTGCTTCTCGCCTGGCCCGT(SEQ ID NO: 46); and 3′ primer AACCTCCCCATCAGCCTACGCTG (SEQ ID NO: 47).The AMIGO sequences were used for homology search with BLAST to findpossible other related sequences. The human AMIGO2 cDNA was cloned fromthe HT1080 cell line (ATCC #CCL-121) as above: the 5′ primer wasCTCAGAGGCGACCATAATGTC (SEQ ID NO: 48) and the 3′ primer wasTGTTTATTTTGCAGACCACACAC (SEQ ID NO: 49). The mouse AMIGO2 cDNA wascloned from adult mouse cerebrum with the following primers: 5′ primerCTCAGAGGCGACCATAATGTC (SEQ ID NO: 50); and 3′ primerGCGATGCTGAAGGCTAAGATG (SEQ ID NO: 51). The human AMIGO3 cDNA was clonedfrom the HEK293 cell line (ATCC #CRL-1573) with the 5′ primerCAACCTGCACAGAGCTGCTCTGTAC (SEQ ID NO: 52) and the 3′ primerGCACAGTGCTTCCCACCAGTATCTG (SEQ ID NO: 53). The mouse AMIGO3 cDNA wascloned from adult mouse cerebellum with the 5′ primerAGAAGTAGGTGAGTCTTGGAGCT (SEQ ID NO: 54) and the 3′ primerTGTTGTGCAGGTAGAGCCTG (SEQ ID NO: 55).

RT-PCR and In Situ Hybridization

Total RNA was reverse transcribed in a reaction containing 1 μg RNA,0.25 mM dNTP-mix, 1 μg random nonamers, 20 U recombinant Rnasin(Promega), 200 U MMLV-RT (Promega) with 1×MMLV reaction buffer supplied.2 μl of the reverse transcription mixture was then used for polymerasechain reaction with gene specific primers. For the mouse AMIGO theprimers where as follows: 5′ primer AGCAACATCCTCAGCTGCTC (SEQ ID NO:56); and 3′ primer CTTCAGCTTGTTGGAGGACAG (SEQ ID NO: 57). For mouseAMIGO2 the primers were: 5′ primer GGCACTTTAGCTCCGTGATG (SEQ ID NO: 58);and 3′ primer GTCTCGTTTAACAGCCGCTG (SEQ ID NO: 59). For the mouse AMIGO3the primers were: 5′ primer AGGTGTCAGAGTCCCGAGTG (SEQ ID NO: 60); and 3′primer GTAGAGCAACACCAGCACCA (SEQ ID NO: 61). For GAPDH control theprimers were: 5′ primer CAACGACCCCTTCATTGACC (SEQ ID NO: 62); and 3′primer AGTGATGGCATGGACTGTGG (SEQ ID NO: 63).

The subsequent PCR reaction was performed in a PCR mix (2.5 μM dNTP, 10mM Tris-HCL, pH 8.8, 150 mM KCL, 1.5 mM MgCl₂, 0.1% Triton X-100)containing 0.2 μM 5′ primer and 3′ primer and 1 unit of DYNAzyme II DNAPolymerase (Finnzymes). The amplification products were separated on1.5% agarose gel and stained with EtBr.

For in situ hybridization with radiolabeled probes, a 1.2-kb fragmentfrom the mouse AMIGO cDNA was PCR amplified with the following primers:5′ primer CCGCTCGAGCCGGCCGATCTGTGGTFAG (SEQ ID NO: 64); and 3′ primerCGGAATTCTCACACCACAATGGGTCTATCAGA (SEQ ID NO: 65). The reaction productwas then ligated into pGEM-T vector. In situ hybridization analysis wascarried out using single-stranded RNA probes on mouse fetal and adultparaffin embedded tissue sections as described previously (Reponen etal., 1994).

Production of AMIGO Ig-Fusion Protein

A 1180-bp BamHI fragment containing the entire extracellular codingregion of the mouse AMIGO was amplified by PCR with the followingprimers: 5′ primer CGGGATCCTAGGGTGACTCTCTCCCAGATCC (SEQ ID NO: 66); and3′ primer CGGGATCCGTTGAGGGTGTCATGGTGTCC (SEQ ID NO: 67). The reactionproduct was then ligated into pRMHA3-3c-FC-cDNA. The AMIGO Ig-fusionprotein plasmid was cotransfected with the hygromycin resistance plasmidp-COP-hyg into Drosophila S2-cells by using the Fugene6 transfectionreagent (ROCHE). After a three weeks selection with 300 μg/ml hygromycinB (Calbiochem), stabile AMIGO Ig-fusion S2-cell pools were cultured inshake flasks where the protein expression was induced with 500 μM CuSO₄.After culturing for 6 days the AMIGO Ig-fusion protein was isolated fromthe supernatant by using protein-A agarose (Upstate) according to themanufacturer's instructions.

Antibodies, Western Blotting and Immunohistochemistry

Rabbit anti-AMIGO peptide antibodies were raised against the syntheticpeptide YAMGETFNET (SEQ ID NO: 68) (corresponding to amino acids 341-350of the mouse AMIGO and 342-351 of the rat and human AMIGO). Binding ofthe antibodies to AMIGO was verified using the recombinant AMIGOIg-fusion protein and crude brain extracts in Western blotting (seebelow). Since the antibodies bound more intensely and specifically tothe rat AMIGO compared to AMIGO from other species (possibly due tospecies differences in the glycosylation site close to the peptidesequence used in immunization), rat samples were primarily used inimmunochemical detections.

Brains of embryonic, postnatal and adult rats were extracted to thefinal concentration of 83.3 mg tissue/ml SDS-extraction buffer (62,5 mMTris, 1,8% SDS, 7,75% glycerol, 4,4% 2-mercaptoethanol, pH 6.8). Afteraddition of the SDS buffer, the extracts were pressed several timesthrough a needle. The extracts were boiled 2×5 min and centrifuged at 10000×g for 10 min to remove nonsoluble material. Samples corresponding tothe same wet weight of tissue were analysed by Western blotting. Ponceaustaining of the membrane confirmed uniform protein amounts.

Precast 4-15% gels (Bio-Rad) were used for SDS-PAGE in Western blotting.Proteins were transferred to Hybond™ nitrocellulose membrane (AmershamPharmacia Biotech) by Semi-dry blotting technique. Rabbit anti-AMIGOpeptide antibody (1/1000 dilution) and monoclonal anti-CNPase, clone11-5B (Sigma, 1/1500) were used as primary antibodies. HRP-conjugatedgoat anti-rabbit IgG (Bio-Rad) and sheep anti-mouse IgG (AP Biotech)were used as secondary antibodies. The antibody comples were detectedusing ECL™ reagents (AP Biotech).

Immunohistochemistry of AMIGO was performed using paraffine sections. Inbrief, adult rats were sacrificed after CO₂ treatment by cervicaldislocation and tissues were fixed by using ice-cold PBS with 4%paraformaldehyde, and the samples were then transferred in paraffine.Hydrated paraffine sections (4-10 μm thick) were incubated with 1%hydrogen peroxide/methanol solution for 20 min, and washed again withPBS. The sections were blocked for 1 h with 5% skimmed milk powder inPBS. The sections were then incubated with the rabbit AMIGO peptideantiserum, which was diluted 1/200 in the blocking buffer at +4° C.overnight. After washing with PBS, the sections were incubated with HRPconjugated goat anti-rabbit antibodies (Biorad) at a dilution of 1:500for 2 h at room temperature, washed with PBS and incubated withaminoethyl carbazole (AEC, Sigma) as a chromogenic substrate.Immunofluorescence staining for in vitro cultured hippocampal neuronswas performed by using FITC conjucated goat anti-rabbit secondaryantibodies (Jackson lab).

Neurite Outgrowth Assay

Hippocampi were dissected from 18-day-old rat embryos into a Ca—Mg-freetrituration medium (HBSS with 1 mM sodium pyruvate and 10 mM HEPES, pH7.4). Cells were dissociated by pipetting 25 times with glass pasteurpipette and washed once with the Ca—Mg-containing buffer (HBSS+Ca+Mgwith 1 mM sodium pyruvate and 10 mM HEPES, pH 7.4). The cells wereseeded at the density of 70000 cells/cm² on 96-well polystyrene dishescoated by the test protein in Neurobasal medium with 2% B27 supplement(GIBCO BRL), 1% BSA, 0.5 mM L-glutamine, 25 μM L-glutamic acid and 1×penicillin-streptomycin. The dishes were coated with the test protein(3.125-100 μg/ml) in PBS overnight at 4° C., washed tree times with PBS,and blocked with 1% BSA in PBS for 1 h at room temperature before addingthe cells. The cells were cultured for 24 h before counting the neuriteoutgrowth. For counting of neurite outgrowth, images were taken fromliving cells using randomly selected microscopic fields and theextensions, which were twice the length of the cell soma, wereconsidered as neurites. For quantification of neurite outgrowth, 15images (275 μm×225 μm) with a total of 750 cells were evaluated fromevery concentration of the test protein (AMIGO Ig-fusion or Fc controlsubstrate) used for coating. The data were pooled from three independentexperiments.

To test the effect of soluble AMIGO Ig-fusion protein the dishes werecoated with the AMIGO Ig-fusion protein (12.5 μg/ml in PBS) at 4° C.overnight, washed three times with PBS, and blocked with 1% BSA in PBSfor 1 h at room temperature. The cells were seeded at the density of70000 cells/cm² and cultured for 24 h before counting the neuriteoutgrowth. Counting was carried out as above from three independentexperiments. A total of 750 cells were evaluated for every concentrationof the test protein (AMIGO Ig-fusion or the Fc control protein) used insolution.

In Vitro Fasciculation Assay

Fasciculation of neurites was studied with hippocampal neurons preparedas above. The 96-well plates were coated with poly-L-lysine at +4° C.overnight, washed three times with PBS, and blocked with 1% BSA in PBSfor 1 h at room temperature. The cells were seeded at the density of70000 cells/cm² in the serum free medium (see “Neurite outgrowth assay”)with either the AMIGO Ig-fusion protein or the Fc control protein insolution. The AMIGO Ig-fusion and the Fc control protein were tested at3.25-25 μg/ml. The experiment was repeated independently 3 times, andpictures were taken from living cells after 4 days in culture. Forquantification of neurite outgrowth, 12 randomly taken images (45 μm×35μm) were taken for every concentration of the AMIGO Ig-fusion and the Fccontrol protein used in solution. To evaluate inhibition offasciculation, the total length of the processes, the diameter of whichis <2 μm (formed only from 1-3 neurites), was measured from the 12images taken for every protein concentration tested.

Pictures for the neurite outgrowth and fasciculation experiments weretaken with Olympus DP10 digital camera. The measurements were carriedout by using the Image-Pro image analysis software.

Binding Assays

Coimmunoprecipitation experiments were performed using transientlytransfected HEK293T cells. The constructs were transfected into thecells by using FUGENE6 (ROCHE) according to the manufacturer'sinstructions. The full length AMIGO was cloned in frame with thepEGFP-N1 (Clontech) and pcDNA6-V5-His (Invitrogen) vectors. The fulllength RAGE was cloned in frame with the pcDNA6-V5-His vector. Aftertransfection, the cells were grown for 48 h before lysing in the RIPAbuffer with 10 mg/ml PMSF and 60 μg/ml aprotinin (SIGMA).Coimmunoprecipitation experiments were carried out using rabbit anti-GFPantibody (Santa Cruz; sc-8334) and mouse anti-V5 antibody (Invitrogen;46-0705) at the concentration of 1 μg/ml.

The aggregation assay was carried out using protein A Fluoresbritecarboxylated beads (Polysciences, size 1 μm). The beads (100 μg) werefirst washed 3 times with PBS, 2% BSA, 0.1% Tween-20 solution and theywere the mixed and sonicated in water bath in 50 μl of the buffermentioned above. The beads were divided to two aliquots, and the testand the control protein (10 μg each) were added into the beads in 25 μlof PBS, 2% BSA and 0.1% Tween-20 solution (final volume 50 μl). Afteraddition of the protein 2 μl samples were taken into 100 μl of PBS, 2%BSA, 0.1% Tween-20 solution in 96-well plate at different time points.The plate was incubated at room temperature and the aggregation wasevaluated under the fluorescence microscope. Kinetics of beadaggregation was calculated from three independent experiments from 12fields containing 1500 beads. The extent of bead aggregation isrepresented by the index N_(t)/N₀ where N_(t) and N₀ are the totalnumber of particles at the incubation times t and 0 (Agarwala et al.,2001).

Coimmunoprecipitation of AMIGO and AMIGO2 with EGFR

Coimmunoprecipitation experiments were performed using stable HEK293cells expressing EGFR. The constructs were transfected into the cells byusing FUGENE6 (ROCHE) according to the manufacturer's instructions. Thefull length and extracellular part (EC-part) AMIGO, AMIGO2 and AMIGO3were cloned in frame pcDNA6-V5-His (Invitrogen) vectors. Aftertransfection, the cells were grown for 48 h before lysing in the RIPAbuffer with 10 mg/ml PMSF, 60 μg/ml aprotinin (SIGMA) and 1 mM EDTA.Coimmunoprecipitation experiments were carried out using rabbitanti-EGFR antibody (Santa Cruz) and mouse anti-V5 antibody (Invitrogen;46-0705) at the concentration of 1 μg/ml.

EGFR Phosphorylation Experiment

EGFR phoshorylation experiments were performed using HEK293T cells. Theconstructs were transfected into the cells by using FUGENE6 (ROCHE)according to the manufacturer's instructions. The full length AMIGO,AMIGO2 and AMIGO3 were cloned in frame with pcDNA6-V5-His vector(Invitrogen). The full length human EGFR was cloned with C-terminalFlag-tag into pcDNA6 vector (Invitrogen). The cells on 50% confluent 6cm plate were transfected with 0.3 μg of EGFR plasmid and with 1.7 μg ofAMIGO, AMIGO2, AMIGO3 or control plasmid (pcDNA6-V5-His, Invitrogen).After 24 hours of transfection cells were starved for 4 hours withoutserum. The autophosphorylation of the EGFR was induced by adding 50ng/ml of EGF for 5 minutes in +37° C. The cells were lysed andimmunoprecipitated with anti-phospho-Tyrosine antibody (clone PY20). Thecells were also immunoprecipitated with anti-Flag-tag antibody (cloneM2). The samples from anti-phospho-Tyrosine immunoprecipitation weredetected on western blot by using the anti-flag-tag antibody to see theEGFR phosphorylation differences between the samples. The samples fromanti-Flag-tag immunoprecipitation were detected on western blot by usingthe anti-phospho-Tyrosine antibody to see the EGFR phosphorylationdifferences between the samples.

Homo- and Heterophilic Binding of AMIGO, AMIGO2 and AMIGO3

Coimmunoprecipitation experiments were performed using transientlytransfected HEK293T cells. The constructs were transfected into thecells by using FUGENE6 (ROCHE) according to the manufacturer'sinstructions. The full length and extracellular part (EC-part) AMIGO,AMIGO2 and AMIGO3 were cloned in frame with the pEGFP-N1 (Clontech) orpcDNA6-V5-His (Invitrogen) vectors. The full length RAGE was cloned inframe with the pcDNA6-V5-His vector. After transfection, the cells weregrown for 48 h before lysing in the RIPA buffer with 10 mg/ml PMSF and60 μg/ml aprotinin (SIGMA).

Coimmunoprecipitation experiments were carried out using rabbit anti-GFPantibody (Santa Cruz; sc-8334) and mouse anti-V5 antibody (Invitrogen;46-0705) at the concentration of 1 μg/ml.

Knockout Constructs for AMIGO, AMIGO2 and AMIGO3.

For AMIGO gene targeting, we constructed a replacement vector by usinggenomic DNA fracments from mouse phage library (strain 129SV). The wholecoding region of AMIGO gene was replaced by inserting Beta-galactosidasegene under the promoter of AMIGO gene using tailored PCR primers: 5′primer GCGGCCGCTCAGGGCCCACGGTTTCTGCAG (SEQ ID NO: 69) (with NotI site)and 3′ primer GGCGCGCCACTGGGAAGAGVGAGGAAGGCCAC (SEQ ID NO: 70) (withAscI site). For positive selection, we cloned the neomycin-resistancegene after the beta-galactosidase gene. The 3′ prime homologous arm wasinserted into the vector as a KpnI/NcoI fragment (NcoI blunted). Thelength of the homologous recombination arms where 9.9 kb for 5′ arm and2.0 kb for 3′ arm.

For AMIGO2 gene targeting, we constructed a replacement vector by usinggenomic DNA fracments from mouse phage library (strain 129SV). The wholecoding region of AMIGO2 gene was replaced by inserting human placentalalkaline phosphatase gene under the promoter of AMIGO2 gene usingtailored PCR primers: 5′ primer TAAACTAGCGGCCGCTCATGGAGGCTCACCCATGGAC(SEQ ID NO: 71) (with NotI site) and 3′ primerAGATATGGCGCGCCGGTCGCCTCTGAGTCTCTTGCCAG (SEQ ID NO: 72) (with AscI site).For positive selection, we cloned the neomycin-resistance gene after thehuman placental alkaline phosphatase gene. The 3′ homologous arm wasinserted into the vector as a BamHI/HindIII fragment (HindIII blunted).The length of the homologous recombination arms where 3.0 kb for 5′ armand 3.0 kb for 3′ arm.

For AMIGO3 gene targeting, we constructed a replacement vector by usinggenomic DNA fracments from mouse phage library (strain 129SV). The wholecoding region of AMIGO3 gene was replaced by inserting EGFP gene underthe promoter of AMIGO3 gene using tailored PCR primers: 5′ primerACCTTAATTAACCAGATGGCTTCTTCTTTC (SEQ ID NO: 73) (with PacI site) and 3′primer AGATATGGCGCGCCAGTGACTACCAGGGAAGAT (SEQ ID NO: 74) (with AscIsite). For positive selection, we cloned the neomycin-resistance geneafter the EGFP gene. The 3′ homologous arm was inserted into the vectoras a BamHI fragment. The length of the homologous recombination armswhere 3.5 kb for 5′ arm and 2.6 kb for 3′ arm.

Using standard procedures, we electroporated R1 mouse embryonic stemcells, suspenced in PBS, with 20 μg linearized (AMIGO:NotI, AMIGO2:NotIand AMIGO3: PacI) targeting vector, using BioRad Gene Pulser (240 V and500° F.). Transfected cells were selected with 300 μg/ml G418 (Gibco).On day 9-11 after electroporation, we picked 100-400 clones andidentified resistant clones with homologous recombination by PCRamplification using primers for neomycin resistance gene and outside thetargeted locus. PCR results were confirmed by using southern blots withprobes outside the targeting locus.

Using standard procedures, selected embryonic stem cells were aggregatedinto ICR morulas and aggregates were transferred to pseudopregnantfoster mothers. Highly chimeric males were bred to ICR females andheterozycos offsprings were intercrossed to obtain homozygous mutantmice. For genotyping the genomic DNA was isolated from tail biopsieswith protein K digestion and isopropanol precipitation. For routinggenotyping, we used PCR where first reaction contains oligos which couldamplificate product only from intact AMIGO, AMIGO2 or AMIGO3 gene locus(from inside the genes). The second PCR reaction contains oligos whichcould only amplificate product from targeted locus (one oligo fromneomycin gene and the second from 3′ homologous arm used for targeting).

These AMIGO, AMIGO2 and AMIGO3 single knockout mice strains have beenused to generate double knockout mice strains (ΔAMIGO/ΔAMIGO2;ΔAMIGO/ΔAMIGO3; ΔAMIGO2/ΔAMIGO3) and triple knockout mouse strain(ΔAMIGO/ΔAMIGO2/ΔAMIGO3) by using standard breeding procedures. Thegenotype of the mutant mice were confirmed by using same PCR reactionsas in single knockout strains.

AMIGO ig-Fusion Transgenic Animals

The DNA region encoding mouse AMIGO extracellular part was amplified byPCR from mouse AMIGO cDNA using the BamHI-containing upstream primerCGGGATCCTAGGGTGACTCTCTCCCAGATCC (SEQ ID NO: 75) and the BamHI-containingdownstream primer CGGGATCCGTTGAGGGTGTCATGGTGTCC (SEQ ID NO: 76). PCRfragment was cloned into frame with human IgG FC-part in expressionvector pRMHA3-3c-FC. The DNA region encoding mouse AMIGO extracellularpart fused with IgG FC-part was amplified by PCR using theNotI-containing upstream primer ATAAGAATGCGGCCGCCAATGTGCATCAGTTGTGGTCAG(SEQ ID NO: 77) and the XbaI-containing downstream primerGCTCTAGACGTGCCAAGCATCCTCGTGCGAC (SEQ ID NO: 78). The PCR fragment wascloned into a vector psisGI. In the resulting plasmid, the open readingframe of AMIGO ig-fusion was located under the control of a PDGF-betapromoter and supplied with the polyadenylation signal of the bovinegrowth hormone. The construct was injected into the pronuclei of oocytesfrom superovulated females of C57BL/6 strain. The transgene integrationwas determined by Southern blot and PCR analyses of tail DNA. Toestablish the transgenic line, founders were crossed with C57BL/6animals.

Regeneration Experiment with AMIGO, AMIGO2 or AMIGO3 Proteins.

Spinal cord injury and delivery of AMIGO, AMIGO2 or AMIGO3 can be madeas follows. BALB-c female mice (n=70) are anesthetized with 0.4 ml/kghypnorm and 5 mg/kg diazepam. A segment of the thoracic spinal cord isexposed using fine rongeurs to remove the bone, and a dorsalover-hemisection was made at T7. Fine scissors are used to cut thedorsal part of the spinal cord, which is cut a second time with a fineknife to ensure that the lesion extends past the central canal. TheSABER Delivery System (DURECT Corporation) is according tomanufacturer's instructions AMIGO, AMIGO2 or AMIGO3 Ig-fusion proteinsare added into the SABER solution in concentration of 1-100 mg/ml. Ascontrols, a second group of animals receives SABRE solution with PBSbuffer, and a third group is left untreated. For retransections 3 weeksafter SCI, the spinal cords are cut at T6 as described above, and theanimals are tested using the Basso-Beattie-Bresnahan (BBB) locomotorrating scale on days 1, 2, and 6 after the second surgery.Alternatively, Ig-fusion protein is replaced with AMIGO ectodomain asdescribed below.

Axonal Regeneration Experiment with Soluble AMIGO, AMIGO2 or AMIGO3Ectodomains.

Spinal cord dorsal hemisection and corticospinal fiber tracing isadapted from GrandPre et al. (2002) Nogo-66 receptor antagonist peptidepromotes axonal regeneration. Nature 417: 547-551. Adult female C57BL/6mice (8-10 weeks of age) are deeply anesthetized with intramuscularketamine (100 mg/kg) and intraperitoneal xylazine (15 mg/kg). A completelaminectomy is performed, and the dorsal part of spinal cord is fullyexposed at levels T6 and T7. The dorsal half of the spinal cord is cutwith a pair of microscissors to sever the dorsal parts of thecorticospinal tracts, and the depth of lesion (approximately 1.0 mm) isassured by passing the sharp part of a number 11 blade across the dorsalhalf of the cord. An osmotic minipump (Alzet model 2002, Alza, MountainView, Calif.) is implanted after the hemisection of dorsal spinal cordand positioned to deliver reagents to the subcutaneous space. A catheterconnected to the outlet of the minipump is inserted into the intrathecalspace of the spinal cord at the T7 level through a small hole in thedura. The pump is filled with vehicle (97.5% PBS plus 2.5% DMSO) orsoluble AMIGO, AMIGO2 and/or AMIGO3 ectodomain in the vehicle. Thevehicle or soluble AMIGO, AMIGO2 and/or AMIGO3 are deliveredcontinuously at a rate of approx 0.6 μl/hr for 14 d and the solubleAMIGO, AMIGO2 and/or AMIGO3 ectodomain doses are 2.0, 7.5 and 15.0mg·kg−1·d−1. For those mice receiving soluble AMIGO, AMIGO2 and/orAMIGO3 ectodomain without spinal cord injury, the laminectomy andminipump placement are accomplished in the same fashion. Two weeks afterlesion, a burr hole is made on each side of the skull overlying thesensorimotor cortex of the lower limbs. The anterograde neuronal tracerbiotin dextran amine (BDA, 10% in PBS) is applied at four injectionsites at a depth of 0.5-0.8 mm from the cortical surface on each side.Two weeks after BDA injection, the animals are killed by perfusion withPBS, followed by 4% paraformadehyde. The spinal cord extending from 6 mmrostral to 6 mm caudal from the lesion site is cut parasaggitally (50μm) on a vibrating microtome. Transverse sections are collected from thespinal cord 8-12 mm rostral to and 8-12 mm caudal to the injury site.The sections are incubated with avidin-biotin-peroxidase complex and theBDA tracer for regenerated axons is visualized by nickel-enhanceddiaminobenzidine HRP reaction. For bevioral analysis vehicle-treated andsoluble AMIGO, AMIGO2 or AMIGO3 ectodomain treated mice are comparedusing the Basso-Beattie-Bresnahan (BBB) locomotor rating scale accordingto Basso et al (1995) A sensitive and reliable locomotor rating scalefor open field testing in rats. J. Neurotrauma 12, 1-21.

Inhibition of Glial Scar Formation in CNS with Soluble AMIGO, AMIGO2 andAMIGO3 Proteins

Stereotactic lesioning of the cerebral cortex and intraventricularcannulation can be made according to (Logan et al., 1994). Adult female200- to 250-g Wistar rats are assigned to two treatment groups of 5animals each receiving: (i) 30 μg/10 μl/day Fc-control protein; or (ii)30 μg/10 μl/day AMIGO, AMIGO2 and/or AMIGO3 Ig-fusion protein in saline.On day 0 of the experiment, a stereotactically defined unilateralincisional lesion is placed through the cerebral cortex into the lateralventricle at the same time as ipsilateral placement of a permanentintraventricular cannula. Reagents (10 μl) are perfused into the lesionsite by daily intraventricular injections through the cannulae for 14days under halothane anaesthesia. After 14 days post lesion (dpl),animals are killed and their brains processed for immunohistochemicalanalysis of the lesion site. Alternatively, Fc-fusion protein isreplaced with AMIGO ectodomain in order to avoid immune response againstFc domain, hence the treatment groups of 5 animals are comprise: (i) 10μl/day phosphate buffered saline (PBS); or (ii) 30 μg/10 μl/day solubleAMIGO, AMIGO2 or AMIGO3 ectodomain in phosphate buffered saline.

Modulation of Tumour Metastasis by Using Soluble AMIGO, AMIGO2 or AMIGO3Extracellular Domain.

The modulation of tumour metastases assay can be performed as follows.Lewis lung murine carcinoma cells are injected into the dorsal midlineof male, 6-8-week-old C57BL/6J mice (Jackson Laboratories, Bar Harbor,Me.). Primary tumours are surgically excised when tumour volume is 1,500mm³ (day 14). For three days before the removal of primary tumor, micereceive AMIGO-, AMIGO2- or AMIGO3 Ig-fusion protein or control FC-partprotein once daily, 21 days after removal of primary tumour. Weight ofthe lungs and numbers of lung surface metastases are determined under ×4magnification using an Olympus microscope after intratracheal injectionof India Ink (15%). Alternatively, animal experiments are adapted fromLiao et al. (2000). For the pulmonary metastasis model, C57BL/6J mice(Jackson Laboratories, Bar Harbor, Me.) are injected intra-footpad with1×10⁵ cells of murine Lewis lung carcinoma. When footpad tumors reach 5mm in diameter, the tumor-bearing leg is surgically ligated. Mice arethen divided into two groups receiving injections of approx 20-30mg/kg/dose of either vehicle (phosphate buffered saline) or vehicle withsoluble AMIGO, AMIGO2 or AMIGO3 ectodomain every 3 days for 3 weeks.Weight of the lungs and numbers of lung surface metastases aredetermined under ×4 magnification using an Olympus microscope afterintratracheal injection of India Ink (15%).

Blockage of Local Tumour Growth with Soluble AMIGO, AMIGO2 or AMIGO3Extracellular Domain.

Rat C6 glioma cells are injected into the dorsal midline of female NCRimmunocompromised mice aged 4-6 weeks (Taconic Farms, Germantown, N.Y.).Alternatively, rat C6 glioma cells are injected into the dorsal midlineof female mice with severe combined immunodeficiency (SCID; TaconicFarms). Administration of AMIGO-, AMIGO2- or AMIGO3 Ig-fusion protein orcontrol FC-part protein is done once daily to immunocompromised (athymicnude) mice upon injection of rat C6 glioma cells. Tumours are measuredat day 21 with calipers and the volume is calculates: V=π*h(h²+3a²)/6,where h=height of the tumour segment; a=(length+width of the tumour)/4;and V=volume of the tumour. Tumour tissue is retrieved, fixed informalin (10%) and paraffin-embedded sections are prepared.Alternatively, Human A431 squamous cell carcinoma xenografts areestablished in athymic nude nu/nu mice, 6-8 weeks of age throughsubcutaneous inoculation of 0.5-2*10⁶ cells into the dorsal flank ofeach mouse. Administration of AMIGO-, AMIGO2- or AMIGO3 Ig-fusionprotein or control FC-part protein (approx 10-40 mg/kg/dose) is doneonce daily to immunocompromised (athymic nude) mice upon injection ofhuman A431 squamous cells. Tumours are measured at day 21 with calipersand the volume is calculates: V=π*h(h+3a²)/6, where h=height of thetumour segment; a=(length+width of the tumour)/4; and V=volume of thetumour. Tumour tissue is retrieved, fixed in formalin (10%) andparaffin-embedded sections are prepared.

Suppression of Tumorigenicity by Lentivirus-Mediated Gene Transfer ofSoluble or Full Length AMIGO, AMIGO2 or AMIGO3

Animal experiments are adapted from Reed et al. (2002) Suppression oftumorigenicity by adenovirus-mediated gene transfer of decorin. Oncogene21:3688-95. Human WiDr colon and A431 squamous cell carcinoma xenograftsare established in athymic nude nu/nu mice, 6-8 weeks of age throughsubcutaneous inoculation of 0.5-2*10⁶ cells into the dorsal flank ofeach mouse. Mice are carefully examined every 2 or 3 days and any tumorgrowth is measured with a micro-caliper according to the followingformula: V=a(b2/2), where a and b represent the larger and smallerdiameters, respectively. When tumors reach 2-3 mm in greater diameter,each mouse receives direct intra-neoplastic injections and also threeother injections 2, 4 and 6 days after first injection. The injectionscontain (approx 50 μl containing 4*10⁷ TU) replication-incompetentlentivirus, either empty virus or virus harboring the full-length AMIGO,AMIGO2 or AMIGO3 or soluble AMIGO, AMIGO2 or AMIGO3 ectodomain gene.Student's two-sided t-test is used to compare the values of the treatedand control samples. A value of P<0.05 is considered as significant.

Animals are sacrificed at the end of the experiments, between 19 and 58days depending on the treatment regimen and inoculum size, and eachtumor is carefully dissected. The tumors are fixed in 10% bufferedformaldehyde, embedded in paraffin and processed for routine histology.To determine the proliferative index of tumor xenografts, the percentageof tumor cell nuclei positive for Ki-67 marker is estimated in 10high-power ('400) fields per animal.

Results

Idenfication and Cloning of a Novel Family of Transmembrane ProteinsContaining a Tandem Array of Leucine-rich Repeats and an ImmunoglobulinDomain (AMIGO, AMIGO2 and AMIGO3)

Ordered differential display (ODD; Matz et al., 1997) was used to searchfor amphoterin-induced genes in neurons. Comparison of ODD fromembryonic day 18 rat hippocampal neurons grown on amphoterin and laminincoated plates revealed a transcript that was expressed more onamphoterin (FIG. 1 A). This expression difference was also confirmedwith RT-PCR (FIG. 1 B).

The sequence of the partial transcript did not give homology with anypreviously cloned genes. By using the 5′ RACE method (Matz et al., 1999)the cDNA encoding the whole coding sequence was cloned (FIG. 2 A). Wenamed this differentially expressed gene as AMIGO (AMphoterin InducedGene and Orphan receptor). Hydrophobicity profile analysis (Nielsen etal., 1997; software SignalIP V2.0.b2) revealed that the protein sequenceof AMIGO contains a putative signal sequence and a putativetransmembrane region. The deduced extracellular part of the proteincontains six leucine-rich repeats (LRRs) and one immunoglobulin domain.The deduced cytosolic part of the protein does not contain any knowndomains.

The human and mouse counterparts of AMIGO were also cloned with the 5′RACE method by using data from the rat AMIGO sequence and from ESTsequences. Identity at the amino acid level between the rat and mouseAMIGO is 95% and the murine sequences are 89% identical to the humanAMIGO. In the extracellular part the most conserved motifs between themurine and human AMIGO are the N-terminal cysteine-rich domain and theLRRs 1-3. Interestingly, the whole transmembrane domain and thecytoplasmic tail are 100% identical between the murine and human AMIGO.

By using homology search we detected ESTs which gave homology but werenot identical as compared to AMIGO. By using these EST sequences wecloned two other novel proteins which we named for convenience as AMIGO2and AMIGO3. The deduced amino acid sequences show that AMIGO2 and AMIGO3have the same domain organization as AMIGO: they also contain a putativesignal seguence for secretion and six LRRs flanked on both the N andC-terminal sides by cysteine-rich LRRNT and LRRCT-domains. Like AMIGO,the deduced extracellular parts of AMIGO2 and AMIGO3 contain animmunoglobulin domain close to the transmembrane domain (for schematicpicture of AMIGO, -2 and -3, see FIG. 2 B).

Similarity at the amino acid level between AMIGO to AMIGO2 is 48%, AMIGOto AMIGO3 is 50% and AMIGO2 to AMIGO3 is 48%. The alignment for AMIGO,-2 and -3 shows that the most conserved regions between the threeproteins are the LRRs, the transmembrane region and some parts of thecytosolic tail (FIG. 2 A). The LRRs found in the AMIGOs can be describedas a motif LX₂LXLX₂NX(L/I)X₂aX₄(F/L/I) (SEQ ID NO: 79) (in which “a”denotes an aliphatic residue and “X” any amino acid); this motifresembles a typical LRR sequence often found in extracellular parts ofanimal proteins (Kajava, 1998).

Expression of the Gene Family Members in Adult Tissues

RT-PCR analysis of adult mouse tissues (FIG. 3) revealed that AMIGO ismainly expressed in the nervous tissues (cerebellum, cerebrum andretina) although some low expression could be also seen in liver,kidney, small intestine, spleen, lung and heart. AMIGO2 expression ismost prominent in cerebellum, retina, liver and lung. A lower AMIGO2mRNA expression is also seen in cerebrum, kidney, small intestine,spleen and testis. AMIGO3 mRNA expression could be detected in everytissue studied showing no specific expression pattern compared to AMIGOor AMIGO2. It thus appears that AMIGO is essentially a nervous systemspecific member of the protein family and we focused on AMIGO in moredetail in the present study.

Cerebrum

In adult rat cerebrum the AMIGO staining was found from many nerve fiberbundles and nerve paths (FIGS. 7 and 9 a). When compared to anti-CNPasestaining, the AMIGO staining co-localizes with almost every myelinatedareas of the cerebrum. In this study the only white matter area whereAMIGO staining was absent was the lateral tractus olfactorius.

However, the AMIGO expression is not restricted to myelinated tracts;for example in hippocampus, non-myelinated tracts in the stratum lucidumCA3 region, which were negative for anti-CNPase and myelin basic protein(myelin basic protein data not shown), stained clearly with anti-AMIGO(FIGS. 9 a and c). In coronal sections staining was restricted in thestratum lucidum of the CA3-region where it was localized more preciselyin basal areas of the apical dendrites of the pyramidal cells (FIG. 8).The anti-AMIGO seemed to stain not the dendrites but the areas aroundthe basal areas of the apical dendrites. In sagital sections the AMIGOstaining was seen to be slightly fibrous (FIGS. 9 c and d). Thelocalization and structure of the AMIGO staining in hippocampus remindsthe one seen for mossy-fibers. The mossy fibers are the axons of thegranule cells from dentatum gyrus, which end up in the stratum lucidumof the CA3-region, where they form synapses with the apical dendrites ofthe pyramidal cells. The mossy-fibers have been shown to stain veryintensively with anti-neurofilament antibodies (Huber et al., 1985).

Our anti-NF-M staining in hippocampus was very similar when compared toanti-AMIGO staining, which supports the interpretation that AMIGOlocalizes in mossy-fibers or structures very closely related to them. Onthe other hand these structures could be the interneuronal axons of theCA3-region, which have been shown to proceed along the mossy-fibers instratum lucidum (Vida and Frotscher, 2000).

In cerebral cortex the AMIGO immunostaining was seen only in particularregions, which were also immunoreactive for anti-CNPase and anti-NF-M(FIG. 7). The cortical staining for all of the three antibodies used(AMIGO, CNPase and NF-M) was diffuse and indistinct, which is related inmyelinated axons. At the same time the AMIGO staining is seen in thebasal areas of the apical dendrites of the cortical pyramidal cells butinterestingly not all of the apical dendrites are AMIGO immunoreactive.The anti-NF-M staining was also found in the apical dendrites but thestaining could also be seen in the cell soma and the basal dendriticareas of the pyramidal cells (FIG. 10).

Cerebellum

In the cerebellum the anti-AMIGO staining was also co-localized with theanti-NF-M staining. In the cerebellum the anti-neurofilament antibodieshave been seen to stain very intensively myelinated axons and basketcell axons (Matus et al., 1979).

The AMIGO staining was intensive in white matter and in the myelinatedaxons of the granular cell layer resembling the one seen for anti-NF-M.The most intensive staining in white matter was found in the middle ofthe cerebellum where the staining was seen in a string of pearls likestructures (FIGS. 11 a and b).

In the cortical areas of the cerebellum the AMIGO staining was seen inboth sides of the Purkinje cell layer. The basket like structure aroundthe Purkinje cell somas were seen to be immunoreactive for AMIGO andthis structure is formed by the basket cell axons (FIG. 11 a and b).

In the molecular layer of the cerebellum the AMIGO staining is seen inthe fibers, which are orientated along the Purkinje cell layer (FIG.11). At least some of these fibers are basket cell axons but also someother axons are AMIGO positive because the AMIGO immunostaining was moreintensive when compared to anti-NF-M staining (data not shown).

Also the nuclei in the middle part of the cerebellum were AMIGOimmunoreactive. In nuclei the AMIGO and NF-M staining differed form eachother because AMIGO staining was only seen in neurites but NF-M stainingcould also be found from neurites and cell soma.

Pons and Medulla Oblongata

In pons and medulla oblongata the AMIGO staining was found in whitematter.

Spinal Cord

In the cross-sections of the spinal cord the anti-AMIGO staining wasseen in the white matter as a dotted like structures. In paraffinsections the myelin sheaths have melted away leaving round holes wherethe myelin has been located. In these sections the AMIGO staining isseen in the dots in the middle of the holes (FIG. 12 a). Also theanti-NF-M antibodies stained these dots (FIG. 12 c) whereas theanti-CNPase did not stained the same structures (FIG. 12 b). Incryosections the AMIGO staining was seen to localize in the middle ofthe myelinated axons and not into the multilayered myelin sheaths (datanot shown.). It is not clear whether all of the AMIGO positive axonswere myelinated or not due to the limitations of the light microscopy.

In the grey matter of the spinal cord the anti-AMIGO stained some nervefibers. Only some fibers of the grey matter, which were crossing intothe white matter, were AMIGO positive. This suggests that AMIGO isexpressed only in some subpopulation of these crossing axons (data notshown).

Kidney, Optic Nerve and Femoral Nerve

The AMIGO staining was found to co-localize with anti-NF-M staining inkidney. The stained structures were defined as autonomous nerve fibers(FIG. 13). The optic nerve was intensively stained with the anti-AMIGOantibodies whereas in femoral nerve the staining was absent (data notshown).

Embryos

In the head of the E18 rat embryo the staining was seen in nerve fibersand in nerve fiber tracts of internal capsule (FIG. 14 c), optic tract(FIG. 14 a), middle cerebellar peduncle, stria medullaris, fasciculusretroflexus and longitudinal fasciculus pons. The AMIGO positivestaining co-localized with anti-NF-M but the CNPase was notimmunohistochemically detectable in E18 embryo (data not shown).

In the whole sections of the E16 embryo anti-AMIGO immunostaining wasfound only in some parts of the developing brain area, in optic nerveand areas close to the intestine and the rib bones (data not shown).

Expression of AMIGO During Development

The AMIGO mRNA expression was studied in more detail using in situhybridization. The AMIGO antisense probe gave a clear signal in thedeveloping and adult nervous tissues whereas the sense probe did notgive any clear signal (sense probe data not shown). A clear AMIGOexpression was already detected in the E13 rodent embryo; at this stagethe highest expression level was found in the dorsal root ganglia andthe trigeminal ganglion with some expression in the central nervoussystem (FIG. 4 A-B). During later stages of development and in theadult, AMIGO was also prominently expressed in the brain, where the mostintense signal was detected in the hippocampus (FIG. 4 C).

To investigate the expression of AMIGO at the protein level, polyclonalantisera were produced against an extracellular 10-amino acid peptidesequence that is found in AMIGO but not in AMIGO 2 or 3. Theanti-peptide antibodies recognized the 75-kD AMIGO Ig-fusion proteinproduced in Drosophila S2 cells (FIG. 5, lanes 1 and 3). Westernblotting of crude brain extracts revealed specific binding to a 65-kDpolypeptide (FIG. 5, lanes 2 and 4). The molecular mass of therecognized polypeptide is close to the calculated molecular mass (56-kD)of AMIGO. Binding of the antibodies to both the fusion protein and the65-kD polypeptide of brain were blocked by the synthetic peptide used asthe immunogen (FIG. 5, lanes 3-6).

Western blotting of AMIGO using crude brain extracts from differentdevelopmental stages was consistent with the in situ hybridization data.The expression appears to start in the brain somewhat later than in theperipheral nervous system and increases clearly between E13 to E14 (FIG.6). The expression is maintained high during the perinatal developmentalstage but is downregulated during the postnatal stages P6 to P10. Afterthis, the expression is again upregulated and remains high in the adultbrain (FIG. 6). Since the time period of the postnatal upregulation ofthe AMIGO expression would appear to coincide with the onset ofmyelination, we compared the expression of AMIGO to that of themyelin-specific marker α-CNPase. Indeed, the expression of AMIGO and theCNPase display a parallel increase during postnatal development (FIG.6). The AMIGO expression thus displays a dual character during braindevelopment; the first expression peak occurs during the late embryonicand perinatal development, and the second increase in expressionaccompanies myelination.

Immunohistochemistry using the anti-peptide antibodies revealed specificstaining only in the nervous system. In general, intensity of theimmunostaining was in agreement with the expression data inferred fromWestern blotting (FIG. 6). Further, specificity of the immunostainingwas suggested by inhibition of antibody binding to tissue sections bythe peptide used as the immunogen (FIG. 5, panel B). In general, AMIGOwas intensely stained in developing and mature fiber tracts. Duringembryonic development when the spinal ganglia express abundantly AMIGOmRNA (see FIG. 4), the immunostaining was observed in the fiber tractsconnecting to the ganglia and the spinal cord but not in the gangliathemselves (FIG. 7, panel A), suggesting that the AMIGO protein istransported to axonal processes. In cerebellum, the most intensestaining was observed in fibers on both sides of the Purkinje celllayer; the characteristic structure formed by the basket cell axonsaround the Purkinje cell soma was clearly discerned by the AMIGOimmunostaining (FIG. 7 B). Consistent with the Western blotting data,AMIGO immunostaining labeled most myelinated axon tracts in the adult.An example is shown in FIG. 7 (panels C and D), demonstrating thesimilarity of the AMIGO and α-CNPase immunostaining around thehippocampus. However, the AMIGO expression is not restricted tomyelinated tracts; for example in hippocampus, non-myelinated tracts inthe stratum lucidum CA3 region, which were negative for α-CNPase (FIG. 7D) and myelin basic protein (data not shown), stained clearly for AMIGO(FIG. 7 C). In general, AMIGO staining was detected (both duringdevelopment and in adult animal) in large-diameter neurites (axons) thatwere also stained by antibodies against the 145 kD neurofilament (datanot shown). As in the forebrain, myelinated axon tracts were alsostained for AMIGO in cerebellum, pons, medulla and spinal cord.

AMIGO was also clearly immunostained both in the cell soma and infasciculated and non-fasciculated processes of cultured hippocampalneurons (FIG. 7 F). As expected from immunostaining of tissue sections,double-immunostaining (not shown) revealed colocalization with the145-kD neurofilament and the β-tubulin (TuJ1) but not with MAP2. AMIGOis thus preferentially expressed in axonal rather than dendriticprocesses.

AMIGO Promotes Neurite Extension of Hippocampal Neurons

Identification of AMIGO from hippocampal neurons growing neurites onamphoterin, the occurrence in fiber tracts in vivo and the domainstructure with LRRs and Ig domains suggest that AMIGO might have a rolein neurite extension. To get insight into the function of AMIGO, wetested if it is able to promote neurite outgrowth of hippocampalneurons. The extracellular part of the AMIGO was fused to human IgG Fcpart, and this fusion protein was immobilized on microtiter wells andused as a substrate for hippocampal neurons. These experiments showedthat the AMIGO Ig-fusion protein promotes attachment and neuriteoutgrowth of hippocampal neurons (FIG. 8 A and C), whereas on the humanIgG Fc control neurite outgrowth was very low or undetectable figure(FIG. 8 B and C). Neurite outgrowth induced by the immobilized AMIGOIg-fusion protein was inhibited by the soluble AMIGO Ig-fusion in theculture medium (FIG. 8 D).

Soluble AMIGO Perturbs Development of Fasciculated Axon Tracts In Vitro

Because AMIGO immunostaining could be found in vitro in hippocampalfasciculating axons and in the axon tracts in vivo, AMIGO mightparticipate in fasciculation of neurites. We addressed this question bya dominant negative approach using the ectodomain of AMIGO as Ig-fusionprotein in the culture medium. Hippocampal neurons were plated onpoly-L-lysine coated wells to promote neurite outgrowth andfasciculation. Microscopy of the cultures revealed that the growthpattern of neurites was dramatically changed in the presence of thesoluble AMIGO. In the control cultures neurites formed fascicles in 4days, where as in the presence of the soluble AMIGO, the processes weremainly non-fasciculated up to at least 5 days in culture (FIG. 9 A-C).

AMIGO Displays a Homophilic Binding Mechanism

Fasciculation of axons is known to involve homophilic interactions andthis might be reason why soluble AMIGO perturbs fasciculation. Wetherefore tested in a coimmunoprecipitation assay wether AMIGO couldbind to itself. To examine AMIGO-AMIGO association, 293 cells werecotransfected with GFP-tagged full length AMIGO (FIG. 10 A, lanes 1-4)and V5-tagged full length AMIGO (FIG. 10 A, lane 1) and solubleV5-tagged AMIGO ectodomain (FIG. 10 A, lane 2). Immunoprecipitation ofboth AMIGO-V5 forms from the cell lysates precipitated AMIGO-GFP (FIG.10 A, lanes 1 and 2) and correspondingly both the full length andsoluble AMIGO-V5 were precipitated with anti-GFP (FIG. 10 A, lanes 1 and2). No coimmunoprecipitation was observed when V5-tagged AMIGO was nottransfected into cells (FIG. 10 A, lane 3). The control proteinV5-tagged human RAGE was not coprecipitated with the AMIGO-GFP and viceversa. (FIG. 10 A, lane 3).

As another approach to study homophilic binding of AMIGO, we added AMIGOIg-fusion protein to protein-A coated beads to get the protein orientedin a manner that occurs at the cell surface. AMIGO caused rapidaggregation of the beads (FIG. 10 B and C), whereas addition of thecontrol protein IgG Fc part into the beads did not induce anyaggregation (FIG. 10 B and D).

Coimmunoprecipitation of AMIGO and AMIGO2 with EGFR The result showsthat both AMIGO and AMIGO2 bind the EGFR and only the EC-part is enoughfor the binding (shown for the AMIGO, FIG. 27).

AMIGO Inhibits EGFR Phosphorylation

When AMIGO and flag-tagged human EGFR are expressed together AMIGO couldclearly inhibit the EGFR autophosphorylation induced by EGF ligationwhen compared to AMIGO2, AMIGO3 and vector control (FIG. 29).

Homo- and Heterophilic Binding of AMIGO, AMIGO2 and AMIGO3

The coimmunoprecipitation results show that AMIGOs could bind eachothers in heterophilically but they also posses homophilic bindingproperties (FIG. 28).

Discussion

A Novel Family of Transmembrane Proteins with Six LRR Domains and OneIg-Like Domain

In this study, we have identified a novel family of transmembraneproteins called AMIGO, AMIGO2 and AMIGO3. These three proteins showclear homology with each other; their length and location of differentdomains are highly identical (FIG. 2 B). This domain relationshipsuggests a common evolutionary origin of the AMIGOs.

Based on genomic sequence data these three proteins probably occur inthe puffer fish Fugu rubripes (data not shown). Interestingly,Drosophila has a protein family called kekkon with three members oftransmembrane proteins kek1, kek2 (Musacchio and Perrimon, 1996) andkek3 (Ashbumer et al., 1999) which show homology in their extracellularparts with the AMIGOs. The extracellular parts of both the AMIGOs andthe kek proteins contain six LRR domains flanked with cysteine-richLRRNT and LRRCT domains and one immunoglobulin domain close to thetransmembrane region. However, the cytoplasmic parts of the AMIGOs andkek proteins do not display homology with each other. The geneexpression data of kek1 and kek2 (Musacchio and Perrimon, 1996) remindsthe one seen for AMIGO and AMIGO2; they all are expressed in the centralnervous system of the adult organism. These domain and expressionsimilarities suggest that the AMIGOs and kek proteins may be derivedfrom a common ancestral gene.

In their extracellular parts the most homologous motifs between theAMIGOs are the LRRs 3-5. The best fit in BLAST searches shows homologywith Slit family of extracellular axon-guiding proteins (Whitford et al2002), and a clear homology is also found with the Nogo-66 receptorwhere the only recognizable motifs are the LRR domains (Fournier et al.2001)(FIG. 11). The similarity found in the LRRs in AMIGO, Slit1 andNogo-66 receptor suggests an evolutionary origin of these proteins froma common ancestor. The clear conservation seen at the LRR area betweenthe AMIGOs suggests that this region is important for interactions withextracellular ligand(s) and that they could also share the same bindingpartner(s).

In the literature there are reports of other transmembrane proteins thatcontain LRRs and Ig domains in the extracellular part of the proteins:ISLR (Nagasawa et al., 1997): 5 LRRs and 1 Ig domain; Pal (Gomi et al.,2000): 5 LRRs and 1 Ig domain; LIG-1 (Suzuki et al., 1996): 15 LRRs and3 Ig domains and GAC1 (Almeida et al., 1998): 12 LRRs and 1 Ig domain.Common for all of these proteins and the AMIGOs is the order of how theLRRs and the Ig domain(s) are organized; the LRRs are always more distalto the transmembrane region than the Ig domain(s). Interestingly, BLASTsearches by using Ig-domain sequences from AMIGOs give no clear homologywith other Ig-domains of the Ig-superfamily proteins but the mostclosest are the ones found in proteins containing both Ig and LRRdomains (data not shown).

Although the cytoplasmic moieties of the AMIGOs do not display any clearhomology with previously identified transmembrane proteins, thealignment of the AMIGOs (FIG. 2 A) shows two conserved serine-richregions; one close to the transmembrane domain and the other at theC-terminus. The C-terminal serine-rich area of AMIGO and AMIGO2 have aconsensus sequence for Casein kinase II (CK2) serine/threonine kinase(Allende et al. 1995) which is ubiquitously expressed in brain butAMIGO3, which is not expressed in the brain, does not have thisconsensus sequence. Recently Watts et al. (1999) showed that thetransmembrane form of TNF-αα has a consensus sequence SXXS which is asubstrate for Casein kinase 1 (CK1) dependent phosphorylation.Interestingly, all three AMIGOs have four possible CK1 phoshorylationsites in these two conserved serine rich areas. Future work will revealwhether these conserved serine residues have important functions insignalling events of the AMIGOs.

There are increasingly reports in the literature and the data banks onmammalian transmembrane proteins with both LRR and Ig domains butunfortunately at present almost all data only comprise the cloning andtissue expression of these proteins. Our data here gives a functionalinsight into these twin motif transmembrane proteins, belonging to boththe LRR and Ig superfamily, in a form of more detailed characterizationof AMIGO.

AMIGO, a Novel Transmembrane Protein in Neuronal Processes withHomophilic Binding Mechanism

Based on RT-PCR experiments, in situ hybridization andimmunohistochemistry, AMIGO is an essentially nervous system specificprotein. Interestingly, AMIGO expression is upregulated at two clearlydistinct stages during brain development: the first peak is foundperinatally, and the second upregulation occurs during or slightlybefore the upregulation of the oligodendrocyte-specific marker α-CNPase.

The first expression peak of AMIGO would be compatible with a role ingrowth of axonal connections. The expression of AMIGO in developing axontracts both in vivo and in vitro and our neurite outgrowth experimentssupport this role. One cellular mechanism in the growth of axonalconnections is fasciculation: axons grow along each other by usingpioneer axons as the substratum for the growth cones of the later ones.Interestingly, a dominant negative approach using AMIGO ectodomain inthe culture medium clearly suggests a role for AMIGO in fasciculation.Further, AMIGO displays a homophilic binding mechanism that wouldexplain its role in fasciculation. Homophilic adhesion moleculesbelonging to both the Ig-superfamily and to the cadherin family havebeen shown to mediate neurite outgrowth and fasciculation during thenervous system development (for reviews, see Kamiguchi and Lemmon 1997;Martinek and Gaul 1997). It is also noteworthy that the LRR sequences ofthe AMIGOs display homology with the slit proteins and with the Nogoreceptor (FIG. 11) that have been implicated in axon growth,regeneration and guidance.

The second upregulation of the AMIGO expression suggests a role inmyelination. It seems reasonable that AMIGO would mediate cell-to-cellinteractions also at this stage of development. However, further studiesare clearly warranted to understand the role of AMIGO in myelinatingaxon tracts, like in the interactions of axons with oligodendrocytes andSchwann cells. Further, AMIGO expression remains high until adulthood.This suggests that AMIGO plays a role in regeneration and plasticity ofthe adult fiber tracts, the mechanisms of which commonly recapitulatemechanisms of fiber tract development.

To get further insight into the functional roles of AMIGO duringdevelopment and adulthood, we have recently targeted the gene in EScells and are currently producing AMIGO null mice (Kuja-Panula andRauvala, unpublished results). In addition to the in vivo approachesusing gene targeting, it will be important to understand what moleculardomains mediate homophilic binding and whether the intracellular domainof AMIGO has signalling properties. Furthermore, future studies willreveal whether the members of the AMIGO family mediate analogouscell-to-cell interactions in non-neuronal tissues characterized in thepresent paper for AMIGO in axonal tracts.

It will be appreciated that the methods of the present invention can beincorporated in the form of a variety of embodiments, only a few ofwhich are disclosed herein. It will be apparent for the specialist inthe field that other embodiments exist and do not depart from the spiritof the invention. Thus, the described embodiments are illustrative andshould not be construed as restrictive.

The publications and other materials used herein to illuminate thebackground of the invention, and in particular, to provide additionaldetails with respect to its practice, are incorporated herein byreference.

REFERENCE LIST FOR EXPERIMENTAL SECTION

-   Agarwala, K. L., S. Ganesh, Y. Tsutsumi, T. Suzuki, K. Amano, and K.    Yamakawa. 2001. Cloning and functional characterization of DSCAML1,    a novel DSCAM-like cell adhesion molecule that mediates homophilic    intercellular adhesion. Biochem. Biophys. Res. Commun. 285:760-772.-   Allende, J. E. and C. C. Allende. 1995. Protein kinases. 4. Protein    kinase CK2: an enzyme with multiple substrates and a puzzling    regulation. FASEB. J. 9:313-323.-   Almeida, A., X. X. Zhu, N. Vogt, R. Tyagi, M. Muleris, A. M.    Dutrillaux, B. Dutrillaux, D. Ross, B. Malfoy, and S. Hanash. 1998.    GAC1, a new member of the leucine-rich repeat superfamily on    chromosome band 1q32.1, is amplified and overexpressed in malignant    gliomas. Oncogene. 16:2997-3002.-   Ashburner, M., S. Misra, J. Roote, S. E. Lewis, R. Blazej, T.    Davis, C. Doyle, R. Galle, R. George, N. Harris, G. Hartzell, D.    Harvey, L. Hong, K. Houston, R. Hoskins, G. Johnson, C. Martin, A.    Moshrefi, M. Palazzolo, M. G. Reese, A. Spradling, G. Tsang, K.    Wan, K. Whitelaw, and S. Celniker. 1999. An exploration of the    sequence of a 2.9-Mb region of the genome of Drosophila    melanogaster: the Adh region. Genetics. 153:179-219.-   Battye, R., A. Stevens, and J. R. Jacobs. 1999. Axon repulsion from    the midline of the Drosophila CNS requires slit function.    Development. 126:2475-2481.-   Battye, R., A. Stevens, R. L. Perry, and J. R. Jacobs. 2001.    Repellent signaling by Slit requires the leucine-rich repeats. J.    Neurosci. 21:4290-4298.-   Brose, K., K. S. Bland, K. H. Wang, D. Arnott, W. Henzel, C. S.    Goodman, M. Tessier-Lavigne, and T. Kidd. 1999. Slit proteins bind    Robo receptors and have an evolutionarily conserved role in    repulsive axon guidance. Cell. 96:795-806.-   Chen, M. S., A. B. Huber, M. E. van der Haar, M. Frank, L.    Schnell, A. A. Spillmann, F. Christ, and M. E. Schwab. 2000. Nogo-A    is a myelin-associated neurite outgrowth inhibitor and an antigen    for monoclonal antibody IN-1. Nature. 403: 434-439.-   Drescher, U., A. Faissner, R. Klein, F. G. Rathjen, and C.    Sturmer. 1997. Axonal growth and pathfinding: from phenomena to    molecules. Cell Tissue Res. 290:187-188.-   Fournier, A. E., T. GrandPre, and S. M. Strittmatter. 2001.    Identification of a receptor mediating Nogo-66 inhibition of axonal    regeneration. Nature. 409:341-346.-   Gomi, F., K. Imaizumi, T. Yoneda, M. Taniguchi, Y. Mori, K.    Miyoshi, J. Hitomi, T. Fujikado, Y. Tano, and M. Tohyama. 2000.    Molecular cloning of a novel membrane glycoprotein, pal,    specifically expressed in photoreceptor cells of the retina and    containing leucine-rich repeat. J. Neurosci. 20:3206-3213.-   Kajava, A. V. 1998. Structural diversity of leucine-rich repeat    proteins. J. Mol. Biol. 277:519-527.-   Kamiguchi, H. and V. Lemmon. 1997. Neural cell adhesion molecule L1:    signaling pathways and growth cone motility. J. Neurosci. Res.    49:1-8.-   Logan, A., M. Berry, A. M. Gonzalez, S. A. Frautschy, M. B. Sporn,    and A. Baird. 1994. Effects of transforming growth factor b1 on scar    production in the injured central nervous system. Eur. J. Neurosci.    6: 355-363.-   Martinek, S. and U. Gaul. 1997. Neural development: how cadherins    zipper up neural circuits. Curr. Biol. 7:R712-R715-   Matz, M., N. Usman, D. Shagin, E. Bogdanova, and S. Lukyanov. 1997.    Ordered differential display: a simple method for systematic    comparison of gene expression profiles. Nucleic Acids Res.    25:2541-2542.-   Muller, S., P. Scaffidi, B. Degryse, T. Bonaldi, L. Ronfani, A.    Agresti, M. Beltrame, and M. E. Bianchi. 2001. New EMBO members'    review: the double life of HMGB1 chromatin protein: architectural    factor and extracellular signal. EMBO. J. 20:4337-4340.-   Musacchio, M. and N. Perrimon. 1996. The Drosophila kekkon genes:    novel members of both the leucine-rich repeat and immunoglobulin    superfamilies expressed in the CNS. Dev. Biol. 178:63-76.-   Nagasawa, A., R. Kubota, Y. Imamura, K. Nagamine, Y. Wang, S.    Asakawa, J. Kudoh, S. Minoshima, Y. Mashima, Y. Oguchi, and N.    Shimizu. 1997. Cloning of the cDNA for a new member of the    immunoglobulin superfamily (ISLR) containing leucine-rich repeat    (LRR). Genomics. 44:273-279.-   Nielsen, H., J. Engelbrecht, S. Brunak, and G. von Heijne. 1997.    Identification of prokaryotic and eukaryotic signal peptides and    prediction of their cleavage sites. Protein Eng. 10: 1-6.-   Pusch, C. M., C. Zeitz, O. Brandau, K. Pesch, H. Achatz, S. Feil, C.    Scharfe, J. Maurer, F. K. Jacobi, A. Pinckers, S. Andreasson, A.    Hardcastle, B. Wissinger, W. Berger, and A. Meindl. 2000. The    complete form of X-linked congenital stationary night blindness is    caused by mutations in a gene encoding a leucine-rich repeat    protein. Nat. Genet. 26:324-327.-   Rauvala, H. and R. Pihlaskari. 1987. Isolation and some    characteristics of an adhesive factor of brain that enhances neurite    outgrowth in central neurons. J. Biol. Chem. 262:16625-16635.-   Rauvala, H., H. J. Huttunen, C. Fages, M. Kaksonen, T. Kinnunen, S.    Imai, E. Raulo, and I. Kilpelainen. 2000. Heparin-binding proteins    HB-GAM (pleiotrophin) and amphoterin in the regulation of cell    motility. Matrix Biol. 19:377-387.-   Reponen, P., C. Sahlberg, C. Munaut, I. Thesleff, and K.    Tryggvason. 1994. High expression of 92-kD type IV collagenase    (gelatinase B) in the osteoclast lineage during mouse    development. J. Cell Biol. 124:1091-1102.-   Schachner, M. 1997. Neural recognition molecules and synaptic    plasticity. Curr. Opin. Cell Biol. 9:627-34-   Stoeckli, E. T. and L. T. Landmesser. 1998. Axon guidance at choice    points. Curr. Opin. Neurobiol. 8:73-79.-   Suzuki, Y., N. Sato, M. Tohyama, A. Wanaka, and T. Takagi. 1996.    cDNA cloning of a novel membrane glycoprotein that is expressed    specifically in glial cells in the mouse brain. LIG-1, a protein    with leucine-rich repeats and immunoglobulin-like domains. J. Biol.    Chem. 271:22522-22527.-   Tessier-Lavigne, M. and C. S. Goodman. 1996. The molecular biology    of axon guidance. Science. 274:1123-1133.-   Van Vactor, D. 1998. Adhesion and signaling in axonal fasciculation.    Curr. Opin. Neurobiol. 8:80-86.-   Walsh, F. S. and P. Doherty. 1997. Neural cell adhesion molecules of    the immunoglobulin superfamily: role in axon growth and guidance.    Annu. Rev. Cell Dev. Biol. 13:425-456.-   Watts, A. D., N. H. Hunt, Y. Wanigasekara, G. Bloomfield, D.    Wallach, B. D. Roufogalis, and G. Chaudhri. 1999. A casein kinase I    motif present in the cytoplasmic domain of members of the tumour    necrosis factor ligand family is implicated in ‘reverse signalling’.    EMBO. J. 18:2119-2126.-   Whitford, K. L., V. Marillat, E. Stein, C. S. Goodman, M.    Tessier-Lavigne, A. Chedotal, and A. Ghosh. 2002. Regulation of    cortical dendrite development by Slit-Robo interactions. Neuron.    33:47-61.

1. A purified and isolated AMIGO nucleic acid comprising a nucleotidesequence that encodes a polypeptide comprising the amino acid sequenceshown in SEQ ID NO:2, 4 or
 6. 2. A purified and isolated nucleic acidcomprising a nucleotide sequence shown in SEQ ID NO:1, 3 or
 5. 3. Apurified and isolated nucleic acid comprising a recombinant nucleotidesequence comprising a nucleotide sequence shown in SEQ ID NO:1, 3 or 5or a homolog or fragment thereof.
 4. An expression construct comprisingthe nucleic acid according to claim 2 operatively linked to anexpression control sequence, said expression construct capable ofencoding an AMIGO polypeptide or variants thereof.
 5. A host celltransformed or transfected with the expression construct of claim
 4. 6.A host cell transformed or transfected with a polynucleotide whereinsaid polynucleotide includes a strand containing a human nucleotidesequence that hybridizes to a DNA comprising the non-coding strandcomplementary to SEQ ID NO:1, 3 or 5, under the following hybridizationconditions: (a) hybridization at 42° C. for 20 hours in a solutioncontaining 50% formamide, 5×SSPE, 5× Denhardt's solution, 0.1% SDS and0.1 mg/ml denatured salmon sperm DNA; and (b) washing the filter twicefor thirty minutes at room temperature and twice for thirty minutes at65° C. with a wash solution containing 1×SSC, and 0.1% SDS.
 7. Anisolated and purified AMIGO polypeptide comprising the amino acidsequence of SEQ ID NO:2, 4 or
 6. 8. Method of producing an AMIGOpolypeptide according to claim 7, said method comprising the steps of:culturing a host cell of claim 5 comprising a polynucleotide encodingsaid polypeptide operably associated with a promoter sequence such thatthe nucleic acid sequence encoding said polypeptide is expressed; andisolating said polypeptide from said host cell or from a growth mediumin which said host cell is cultured.
 9. Method of producing antibodiescomprising: immunising a mammal with the isolated and purified AMIGOprotein of claim 7 or an antigenic fragment thereof.
 10. Use of theisolated and purified AMIGO protein of claim 7 or an antigenic fragmentthereof as an antigen.
 11. An antibody produced by the method of claim9.
 12. The antibody of claim 11 which is labeled with a detectablelabel.
 13. A kit of reagents for use in detecting the presence of AMIGOor allelic variant thereof in a biological sample, comprising acontainer; and in said container: a compound, preferably labeled,capable of detecting AMIGO or allelic variants thereof.
 14. The kitaccording to claim 13, wherein said compound is a primer or probe. 15.The kit according to claim 13, wherein said compound is an antibody asdefined in claim
 11. 16. The kit according to claim 13 for assessing thepredisposition of an individual to a condition mediated by variation ordysfunction of AMIGO.
 17. The kit according to claim 16 furthercomprising instructions for using the kit.
 18. A transgenic non-humananimal containing a human or murine AMIGO gene as a transgene.
 19. Atransgenic non-human animal containing a transgene or insertiondisrupting expression of an AMIGO gene or a homolog thereof.
 20. Apharmaceutical compound comprising AMIGO nucleic acid molecule, AMIGOprotein, AMIGO peptide fragment, AMIGO fusion protein, AMIGO agonists,AMIGO antagonists or anti-AMIGO antibody.
 21. Method for treatment of acondition dependent on AMIGO wherein a pharmaceutically effective amountof the compound of claim 20 is administered to a patient in need of suchtreatment.
 22. Method for affinity purification of ligand that binds tothe AMIGO comprising the following steps: a) contacting a source ofAMIGO receptor with an immobilized AMIGO under conditions whereby theAMIGO receptor to be purified is selectively adsorbed onto theimmobilized AMIGO; (b) washing the immobilized AMIGO and its support toremove non-adsorbed material; and (c) eluting the AMIGO receptormolecules from the immobilized AMIGO to which they are adsorbed with anelution buffer.
 23. A method for identifying a modulator of bindingbetween an AMIGO receptor and an AMIGO receptor, comprising steps of:(a) contacting an AMIGO receptor composition with an AMIGO compositionin the presence and in the absence of a putative modulator compound; (b)detecting binding between AMIGO receptor and the AMIGO receptor in thepresence and absence of the putative modulator; and (c) identifying amodulator compound in view of decreased or increased binding between theAMIGO receptor and the AMIGO receptor in the presence of the putativemodulator, as compared to binding in the absence of the putativemodulator.
 24. A method according to claim 23, further comprising a stepof: (d) making a modulator composition by formulating a modulatoridentified according to step (c) in a pharmaceutically acceptablecarrier.
 25. A method according to claim 24, further comprising a stepof: (e) administering the modulator composition to an animal thatcomprises cells that express the AMIGO receptor, and determiningphysiological effects of the modulator composition in the animal.
 26. Amethod according to claim 23, wherein the AMIGO receptor compositioncomprises a member selected from the group consisting of: (a) a purifiedpolypeptide comprising a AMIGO receptor extracellular domain fragmentthat binds the AMIGO; (b) a phospholipid membrane containing AMIGOreceptor polypeptides; and (c) a cell recombinantly modified to expressincreased amounts of an AMIGO receptor on its surface.
 27. A methodaccording to claim 23, wherein the AMIGO receptor composition comprisesan AMIGO receptor extracellular domain fragment bound to a solidsupport.
 28. A method according to claim 23, wherein the AMIGO receptorcomposition comprises an AMIGO receptor extracellular domain fragmentfused to an immunoglobulin Fc fragment.
 29. A method according to claim23, wherein the AMIGO receptor is selected from the group consisting ofa mammalian AMIGO, AMIGO2, and AMIGO3.
 30. A method according to claim23, wherein the AMIGO receptor is human.
 31. A method according to claim23, wherein the AMIGO composition comprises a member selected from thegroup consisting of: (a) a purified polypeptide comprising an AMIGOfragment that binds the AMIGO receptor; (b) a phospholipid membranecontaining AMIGO polypeptides; and (c) a cell recombinantly modified toexpress increased amounts of an AMIGO on its surface.
 32. A methodaccording to claim 23, wherein the AMIGO composition comprises an AMIGOextracellular domain fragment bound to a solid support.
 33. A methodaccording to claim 23, wherein the AMIGO composition comprises an AMIGOextracellular domain fragment fused to an immunoglobulin Fc fragment.34. A method according to claim 23, wherein the AMIGO is human.
 35. Amethod according to claim 23, wherein the AMIGO receptor compositioncomprises a cell recombinantly modified to express increased amounts ofan AMIGO receptor on its surface, and wherein the detecting stepcomprises measuring an AMIGO binding-induced physiological change in thecell.
 36. A method according to claim 23, wherein the AMIGO compositioncomprises a cell recombinantly modified to express increased amounts ofan AMIGO on its surface, and wherein the detecting step comprisesmeasuring an AMIGO binding-induced physiological change in the cell. 37.A method for screening for selectivity of a modulator of binding betweenan AMIGO and an EGFR, comprising steps of: a) contacting an AMIGOreceptor composition with an EGFR composition in the presence and in theabsence of a compound that modulates binding between the AMIGO receptorand EGFR receptor; and b) detecting binding between the AMIGO receptorcomposition and the EGFR receptor composition in the presence andabsence of the modulator compound, c) identifying the selectivity of themodulator compound in view of decreased or increased binding between theAMIGO receptor and the EGFR receptor in the presence as compared to theabsence of the modulator, wherein increased selectivity of the modulatorfor modulating AMIGO EGFR binding correlates with decreased differencesin AMIGO-EGFR binding.
 38. A method of modulating growth, migration,axonal growth, myelination, fasciculation or proliferation of cells in amammalian organism, comprising a step of: (a) identifying a mammalianorganism having cells that express a AMIGO receptor and/or EGFR; and (b)administering to said mammalian organism a composition, said compositioncomprising an agent selected from the group consisting of: (i) apolypeptide comprising an AMIGO receptor that binds to the AMIGOreceptor and/or EGFR, or a nucleic acid encoding said polypeptide; (ii)a polypeptide comprising a fragment of the AMIGO, wherein thepolypeptide and fragment retain AMIGO binding characteristics of theAMIGO, or a nucleic acid encoding said polypeptide; (iii) an antibodythat specifically binds the polypeptide of (i) or (ii) in a manner thatinhibits the polypeptide from binding the AMIGO receptor and/or EGFR, ora fragment of the antibody that specifically binds the polypeptide of(i) or (ii); (iv) a polypeptide comprising an antigen-binding fragmentof (iii) and that inhibits the polypeptide of (i) or (ii) from bindingthe AMIGO receptor and/or EGFR; (v) a molecule that selectively inhibitsAMIGO binding to the AMIGO receptor without inhibiting AMIGO binding tothe EGFR receptor; and (vi) a molecule selectively binding to the AMIGOreceptor and the EGFR receptor; wherein the composition is administeredin an amount effective to modulate growth, migration, or proliferationof cells that express AMIGO in the mammalian organism.
 39. A methodaccording to claim 38, wherein the mammalian organism is human.
 40. Amethod according to claim 38, wherein the cells comprise neuronal cells.41. A method according to claim 38, wherein the organism has a diseasecharacterized by aberrant growth, migration, or proliferation ofneuronal cells/neuronal extensions.
 42. A method according to claim 38,wherein the conditions comprises a neuronal trauma.
 43. A methodaccording to claim 38, further comprising administering a second agentto the patient for modulating neuronal growth, migration, regenerationor proliferation, said second agent selected from the group consistingof: an antibody that specifically binds with any of the foregoingpolypeptides, an antibody that specifically binds with a receptor forany of the foregoing polypeptides, or a polypeptide comprising anantigen binding fragment of such antibodies.
 44. A method according toclaim 38, wherein the AMIGO extracellular fragment is conjugated with Fcdomain.
 45. A method according to claim 44, wherein rat AMIGO Fc fusionprotein sequences have been replaced essentially with the human AMIGOand Fc sequences
 46. A polypeptide according to claim 38, for use in themanufacture of a medicament for the treatment of diseases characterizedby aberrant growth, migration, regeneration or proliferation of cellsthat express an AMIGO receptor.
 47. Method according to claim 38 whereinneuronal cells are selected from the group consisting of: hippocampalcells, cerebral cells, cerebellar cells, neuronal trauma cells, glialscar cells, spinal cord cells, optic nerve cells, retina cells, kidneycells, and cells acting during fasciculation, guidance, growth, ormyelination.
 48. A method of modulating cancer, tumour growth ormetastasis in a mammalian organism, comprising a step of: (a)identifying a mammalian organism having cells that express an AMIGOreceptor and/or EGFR; and (b) administering to said mammalian organism acomposition, said composition comprising an agent selected from thegroup consisting of: (i) a polypeptide comprising an AMIGO receptor thatbinds to the AMIGO receptor and/or EGFR, or a nucleic acid encoding saidpolypeptide; (ii) a polypeptide comprising a fragment of the AMIGO,wherein the polypeptide and fragment retain AMIGO bindingcharacteristics of the AMIGO, or a nucleic acid encoding saidpolypeptide; (iii) an antibody that specifically binds the polypeptideof (i) or (ii) in a manner that inhibits the polypeptide from bindingthe AMIGO receptor and/or EGFR, or a fragment of the antibody thatspecifically binds the polypeptide of (i) or (ii); (iv) a polypeptidecomprising an antigen-binding fragment the (iii) and that inhibits thepolypeptide of (i) or (ii) from binding the AMIGO receptor and/or EGFR;(v) a molecule that selectively inhibits AMIGO binding to the AMIGOreceptor without inhibiting AMIGO binding to the EGFR receptor; and (vi)a molecule selectively binding to the AMIGO receptor and the EGFRreceptor; wherein the composition is administered in an amount effectiveto modulate cancer growth or metastasis of cells that express AMIGO inthe mammalian organism.
 49. A method according to claim 48, wherein themammalian organism is human.
 50. A method according to claim 48 or 49,wherein the cells comprise glioma, glioblastoma, astrocytoma, anaplasticastrocytoma, ependymomas, oligodendrogliomas, medulloblastomas,meningiomas, schwannomas, craniopharyngiomas, germ cell tumors,pineoblastoma, pineocytoma, germinoma cells, lung carcinoma, breastcarcinoma, ovarian carcinoma, colorectal carcinoma, bladder carcinoma,pancreatic carcinoma, squamous cell carcinoma, or renal carcinoma cells.51. A method according to claim 48, wherein the organism has a diseasecharacterized by cancer or metastasis.
 52. A method according to claim51, wherein the condition comprises a brain tumor.
 53. A methodaccording to claim 48, further comprising administering a second agentto the patient for modulating cancer growth or metastatic growth ofcancer, said second agent selected from the group consisting of: anantibody that specifically binds with any of the foregoing polypeptides,an antibody that specifically binds with a receptor for any of theforegoing polypeptides, or a polypeptide comprising an antigen bindingfragment of such antibodies.
 54. A method according to claim 48, whereinthe AMIGO extracellular fragment is conjugated with Fc domain.
 55. Amethod according to claim 48, wherein rat AMIGO Fc fusion proteinsequences have been replaced essentially with the human AMIGO and Fcsequences
 56. Method for treatment of cancer or metastatic growth ofcancer cells selected from the group consisting of: glioma,glioblastoma, astrocytoma, anaplastic astrocytoma, ependymomas,oligodendrogliomas, medulloblastomas, meningiomas, schwannomas,craniopharyngiomas, germ cell tumors of germinoma cells, lung carcinoma,breast carcinoma, ovarian carcinoma, colorectal carcinoma, bladdercarcinoma, pancreatic carcinoma, squamous cell carcinoma, and renalcarcinoma, comprising a step of administering to a subject in need ofsuch treatment the compound as claimed in claim
 20. 57. Method fortreatment of neuronal cells selected from the group consisting of:hippocampal cells, cerebral cells, cerebellar cells, neuronal traumacells, glial scar cells, spinal cord cells, optic nerve cells, retinacells, kidney cells, and cells acting during fasciculation, guidance,growth, or myelination, comprising a step of administering to a subjectin need of such treatment the compound as claimed in claim
 20. 58. Apolypeptide or a nucleic acid encoding said polypeptide, saidpolypeptide comprising a fragment of an AMIGO that binds to an AMIGOreceptor, for use in the manufacture of a medicament for the treatmentof diseases characterized by aberrant growth, migration, regeneration orproliferation of cells that express an AMIGO receptor.
 59. A method ofmodulating the phosphorylation of a human epidermal growth factorreceptor in cells or tissues comprising contacting said cells or tissueswith the AMIGO compounds.
 60. The method of claim 59, wherein said AMIGOcompounds comprises AMIGO peptides encoded a nucleotide sequenceselected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, and SEQID NO:5.
 61. The method of claim 59, wherein said AMIGO compoundscomprise an anti-AMIGO antibody.